diff --git a/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts b/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
index 264c7a9d981..658b1f564f1 100644
--- a/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
+++ b/packages/app/src/cli/services/app/patch-app-configuration-file.test.ts
@@ -1,4 +1,9 @@
-import {patchAppConfigurationFile, patchAppHiddenConfigFile} from './patch-app-configuration-file.js'
+import {
+  patchAppHiddenConfigFile,
+  setAppConfigValue,
+  unsetAppConfigValue,
+  setManyAppConfigValues,
+} from './patch-app-configuration-file.js'
 import {getAppVersionedSchema} from '../../models/app/app.js'
 import {loadLocalExtensionsSpecifications} from '../../models/extensions/load-specifications.js'
 import {readFile, writeFileSync, inTemporaryDirectory} from '@shopify/cli-kit/node/fs'
@@ -33,150 +38,6 @@ function writeDefaulToml(tmpDir: string) {
   return configPath
 }
 
-describe('patchAppConfigurationFile', () => {
-  test('updates existing configuration with new values and adds new top-levelfields, replaces arrays', async () => {
-    await inTemporaryDirectory(async (tmpDir) => {
-      const configPath = writeDefaulToml(tmpDir)
-      const patch = {
-        name: 'Updated App Name',
-        application_url: 'https://example.com',
-        access_scopes: {
-          use_legacy_install_flow: false,
-        },
-        auth: {
-          redirect_urls: ['https://example.com/redirect3', 'https://example.com/redirect4'],
-        },
-      }
-
-      await patchAppConfigurationFile({path: configPath, patch, schema})
-
-      const updatedTomlFile = await readFile(configPath)
-      expect(updatedTomlFile)
-        .toEqual(`# Learn more about configuring your app at https://shopify.dev/docs/apps/tools/cli/configuration
-
-client_id = "12345"
-name = "Updated App Name"
-application_url = "https://example.com"
-embedded = true
-
-[access_scopes]
-# Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
-use_legacy_install_flow = false
-
-[auth]
-redirect_urls = [
-  "https://example.com/redirect3",
-  "https://example.com/redirect4"
-]
-
-[webhooks]
-api_version = "2023-04"
-`)
-    })
-  })
-
-  test('Adds new table to the toml file', async () => {
-    await inTemporaryDirectory(async (tmpDir) => {
-      const configPath = writeDefaulToml(tmpDir)
-      const patch = {
-        application_url: 'https://example.com',
-        build: {
-          dev_store_url: 'example.myshopify.com',
-        },
-      }
-
-      await patchAppConfigurationFile({path: configPath, patch, schema})
-
-      const updatedTomlFile = await readFile(configPath)
-      expect(updatedTomlFile)
-        .toEqual(`# Learn more about configuring your app at https://shopify.dev/docs/apps/tools/cli/configuration
-
-client_id = "12345"
-name = "app1"
-application_url = "https://example.com"
-embedded = true
-
-[access_scopes]
-# Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
-use_legacy_install_flow = true
-
-[auth]
-redirect_urls = [
-  "https://example.com/redirect",
-  "https://example.com/redirect2"
-]
-
-[webhooks]
-api_version = "2023-04"
-
-[build]
-dev_store_url = "example.myshopify.com"
-`)
-    })
-  })
-
-  test('Adds a new field to a toml table, merging with exsisting values', async () => {
-    await inTemporaryDirectory(async (tmpDir) => {
-      const configPath = writeDefaulToml(tmpDir)
-      const patch = {
-        application_url: 'https://example.com',
-        access_scopes: {
-          scopes: 'read_products',
-        },
-      }
-
-      await patchAppConfigurationFile({path: configPath, patch, schema})
-
-      const updatedTomlFile = await readFile(configPath)
-      expect(updatedTomlFile)
-        .toEqual(`# Learn more about configuring your app at https://shopify.dev/docs/apps/tools/cli/configuration
-
-client_id = "12345"
-name = "app1"
-application_url = "https://example.com"
-embedded = true
-
-[access_scopes]
-# Learn more at https://shopify.dev/docs/apps/tools/cli/configuration#access_scopes
-use_legacy_install_flow = true
-scopes = "read_products"
-
-[auth]
-redirect_urls = [
-  "https://example.com/redirect",
-  "https://example.com/redirect2"
-]
-
-[webhooks]
-api_version = "2023-04"
-`)
-    })
-  })
-
-  test('does not validate the toml if no schema is provided', async () => {
-    await inTemporaryDirectory(async (tmpDir) => {
-      const configPath = joinPath(tmpDir, 'shopify.app.toml')
-      writeFileSync(
-        configPath,
-        `
-random_toml_field = "random_value"
-`,
-      )
-      const patch = {name: 123}
-
-      await patchAppConfigurationFile({path: configPath, patch, schema: undefined})
-
-      const updatedTomlFile = await readFile(configPath)
-      expect(updatedTomlFile)
-        .toEqual(`# Learn more about configuring your app at https://shopify.dev/docs/apps/tools/cli/configuration
-
-random_toml_field = "random_value"
-name = 123
-`)
-    })
-  })
-})
-
 describe('patchAppHiddenConfigFile', () => {
   test('creates a new hidden config file when it does not exist', async () => {
     await inTemporaryDirectory(async (tmpDir) => {
@@ -257,3 +118,176 @@ describe('patchAppHiddenConfigFile', () => {
     })
   })
 })
+
+describe('setAppConfigValue', () => {
+  test('sets a top-level value in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setAppConfigValue(configPath, 'name', 'Updated App Name', schema)
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('name = "Updated App Name"')
+    })
+  })
+
+  test('sets a nested value in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setAppConfigValue(configPath, 'build.dev_store_url', 'example.myshopify.com', schema)
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('[build]')
+      expect(updatedTomlFile).toContain('dev_store_url = "example.myshopify.com"')
+    })
+  })
+
+  test('sets a deeply nested value in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setAppConfigValue(configPath, 'build.auth.settings', true, schema)
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('[build.auth]')
+      expect(updatedTomlFile).toContain('settings = true')
+    })
+  })
+})
+
+describe('unsetAppConfigValue', () => {
+  test('unsets a top-level value in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await unsetAppConfigValue(configPath, 'name', schema)
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).not.toContain('name = "app1"')
+    })
+  })
+
+  test('unsets a nested value in existing table in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      // Add a value first
+      await setAppConfigValue(configPath, 'build.dev_store_url', 'example.myshopify.com', schema)
+
+      // Now unset it
+      await unsetAppConfigValue(configPath, 'build.dev_store_url', schema)
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('[build]')
+      expect(updatedTomlFile).not.toContain('dev_store_url = "example.myshopify.com"')
+    })
+  })
+})
+
+describe('setManyAppConfigValues', () => {
+  test('sets multiple top-level values in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setManyAppConfigValues(
+        configPath,
+        [
+          {keyPath: 'name', value: 'Updated App Name'},
+          {keyPath: 'client_id', value: '67890'},
+        ],
+        schema,
+      )
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('name = "Updated App Name"')
+      expect(updatedTomlFile).toContain('client_id = "67890"')
+    })
+  })
+
+  test('sets a mix of top-level and nested values in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setManyAppConfigValues(
+        configPath,
+        [
+          {keyPath: 'name', value: 'Updated App Name'},
+          {keyPath: 'build.dev_store_url', value: 'example.myshopify.com'},
+        ],
+        schema,
+      )
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('name = "Updated App Name"')
+      expect(updatedTomlFile).toContain('[build]')
+      expect(updatedTomlFile).toContain('dev_store_url = "example.myshopify.com"')
+    })
+  })
+
+  test('properly handles array values in the configuration', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setManyAppConfigValues(
+        configPath,
+        [{keyPath: 'auth.redirect_urls', value: ['https://example.com/redirect3', 'https://example.com/redirect4']}],
+        schema,
+      )
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('[auth]')
+      expect(updatedTomlFile).toContain('redirect_urls = [')
+      expect(updatedTomlFile).toContain('"https://example.com/redirect3"')
+      expect(updatedTomlFile).toContain('"https://example.com/redirect4"')
+      expect(updatedTomlFile).not.toContain('"https://example.com/redirect"')
+      expect(updatedTomlFile).not.toContain('"https://example.com/redirect2"')
+    })
+  })
+
+  test('combines multiple nested keys into a single object structure', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setManyAppConfigValues(
+        configPath,
+        [
+          {keyPath: 'build.dev_store_url', value: 'example.myshopify.com'},
+          {keyPath: 'build.automatically_update_urls_on_dev', value: true},
+        ],
+        schema,
+      )
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('[build]')
+      expect(updatedTomlFile).toContain('dev_store_url = "example.myshopify.com"')
+      expect(updatedTomlFile).toContain('automatically_update_urls_on_dev = true')
+    })
+  })
+
+  test('updates existing configuration with new values and replaces arrays', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const configPath = writeDefaulToml(tmpDir)
+
+      await setManyAppConfigValues(
+        configPath,
+        [
+          {keyPath: 'name', value: 'Updated App Name'},
+          {keyPath: 'application_url', value: 'https://example.com'},
+          {keyPath: 'access_scopes.use_legacy_install_flow', value: false},
+          {keyPath: 'auth.redirect_urls', value: ['https://example.com/redirect3', 'https://example.com/redirect4']},
+        ],
+        schema,
+      )
+
+      const updatedTomlFile = await readFile(configPath)
+      expect(updatedTomlFile).toContain('name = "Updated App Name"')
+      expect(updatedTomlFile).toContain('application_url = "https://example.com"')
+      expect(updatedTomlFile).toContain('use_legacy_install_flow = false')
+      expect(updatedTomlFile).toContain('redirect_urls = [')
+      expect(updatedTomlFile).toContain('"https://example.com/redirect3"')
+      expect(updatedTomlFile).toContain('"https://example.com/redirect4"')
+      expect(updatedTomlFile).not.toContain('"https://example.com/redirect"')
+    })
+  })
+})
diff --git a/packages/app/src/cli/services/app/patch-app-configuration-file.ts b/packages/app/src/cli/services/app/patch-app-configuration-file.ts
index 46cddbf22dc..8a44b8a42bf 100644
--- a/packages/app/src/cli/services/app/patch-app-configuration-file.ts
+++ b/packages/app/src/cli/services/app/patch-app-configuration-file.ts
@@ -22,8 +22,9 @@ export interface PatchTomlOptions {
  * @param path - The path to the app configuration file.
  * @param patch - The patch to apply to the app configuration file.
  * @param schema - The schema to validate the patch against. If not provided, the toml will not be validated.
+ * @internal Internal function, use setAppConfigValue, unsetAppConfigValue, or setManyAppConfigValues instead
  */
-export async function patchAppConfigurationFile({path, patch, schema}: PatchTomlOptions) {
+async function patchAppConfigurationFile({path, patch, schema}: PatchTomlOptions) {
   const tomlContents = await readFile(path)
   const configuration = decodeToml(tomlContents)
 
@@ -41,6 +42,89 @@ export async function patchAppConfigurationFile({path, patch, schema}: PatchToml
   await writeFile(path, encodedString)
 }
 
+/**
+ * Sets a single value in the app configuration file based on a dotted key path.
+ *
+ * @param path - The path to the app configuration file.
+ * @param keyPath - The dotted key path to set the value at (e.g. 'build.dev_store_url')
+ * @param value - The value to set
+ * @param schema - The schema to validate the patch against. If not provided, the toml will not be validated.
+ */
+export async function setAppConfigValue(path: string, keyPath: string, value: unknown, schema?: zod.AnyZodObject) {
+  const patch = createPatchFromDottedPath(keyPath, value)
+  await patchAppConfigurationFile({path, patch, schema})
+}
+
+/**
+ * Sets multiple values in the app configuration file.
+ *
+ * @param path - The path to the app configuration file
+ * @param configValues - Array of keyPath and value pairs to set
+ * @param schema - The schema to validate the patch against. If not provided, the toml will not be validated.
+ *
+ * @example
+ * ```ts
+ * await setManyAppConfigValues('shopify.app.toml', [
+ *   { keyPath: 'application_url', value: 'https://example.com' },
+ *   { keyPath: 'auth.redirect_urls', value: ['https://example.com/callback'] }
+ * ], schema)
+ * ```
+ */
+export async function setManyAppConfigValues(
+  path: string,
+  configValues: {keyPath: string; value: unknown}[],
+  schema?: zod.AnyZodObject,
+) {
+  const patch = configValues.reduce((acc, {keyPath, value}) => {
+    const valuePatch = createPatchFromDottedPath(keyPath, value)
+    return deepMergeObjects(acc, valuePatch, replaceArrayStrategy)
+  }, {})
+
+  await patchAppConfigurationFile({path, patch, schema})
+}
+
+/**
+ * Unsets a value in the app configuration file based on a dotted key path.
+ *
+ * @param path - The path to the app configuration file.
+ * @param keyPath - The dotted key path to unset (e.g. 'build.include_config_on_deploy')
+ * @param schema - The schema to validate the patch against. If not provided, the toml will not be validated.
+ */
+export async function unsetAppConfigValue(path: string, keyPath: string, schema?: zod.AnyZodObject) {
+  const patch = createPatchFromDottedPath(keyPath, undefined)
+  await patchAppConfigurationFile({path, patch, schema})
+}
+
+/**
+ * Creates a patch object from a dotted key path and a value
+ * For example, 'build.dev_store_url' with value 'example.myshopify.com'
+ * will create \{ build: \{ dev_store_url: 'example.myshopify.com' \} \}
+ */
+function createPatchFromDottedPath(keyPath: string, value: unknown): {[key: string]: unknown} {
+  const keys = keyPath.split('.')
+  if (keys.length === 1) {
+    return {[keyPath]: value}
+  }
+
+  const obj: {[key: string]: unknown} = {}
+  let currentObj = obj
+
+  for (let i = 0; i < keys.length - 1; i++) {
+    const key = keys[i]
+    if (key) {
+      currentObj[key] = {}
+      currentObj = currentObj[key] as {[key: string]: unknown}
+    }
+  }
+
+  const lastKey = keys[keys.length - 1]
+  if (lastKey) {
+    currentObj[lastKey] = value
+  }
+
+  return obj
+}
+
 export function replaceArrayStrategy(_: unknown[], newArray: unknown[]): unknown[] {
   return newArray
 }
diff --git a/packages/app/src/cli/services/context.test.ts b/packages/app/src/cli/services/context.test.ts
index 84fb72cf80b..447dd691424 100644
--- a/packages/app/src/cli/services/context.test.ts
+++ b/packages/app/src/cli/services/context.test.ts
@@ -7,7 +7,7 @@ import {createExtension} from './dev/create-extension.js'
 import {CachedAppInfo} from './local-storage.js'
 import link from './app/config/link.js'
 import {fetchSpecifications} from './generate/fetch-extension-specifications.js'
-import * as patchAppConfigurationFile from './app/patch-app-configuration-file.js'
+import * as patchAppConfigurationFileModule from './app/patch-app-configuration-file.js'
 import {DeployOptions} from './deploy.js'
 import {isServiceAccount, isUserAccount} from './context/partner-account-info.js'
 import {
@@ -135,6 +135,13 @@ vi.mock('./context/partner-account-info.js')
 vi.mock('./generate/fetch-extension-specifications.js')
 vi.mock('./app/select-app.js')
 vi.mock('../utilities/developer-platform-client.js')
+vi.mock('./app/patch-app-configuration-file.js', () => {
+  return {
+    patchAppConfigurationFile: vi.fn(),
+    setAppConfigValue: vi.fn(),
+    unsetAppConfigValue: vi.fn(),
+  }
+})
 
 beforeAll(async () => {
   const localSpecs = await loadSpecifications.loadLocalExtensionsSpecifications()
@@ -190,9 +197,7 @@ describe('ensureDeployContext', () => {
     vi.mocked(renderConfirmationPrompt).mockResolvedValue(true)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
 
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
     const metadataSpyOn = vi.spyOn(metadata, 'addPublicMetadata').mockImplementation(async () => {})
 
     // When
@@ -203,14 +208,11 @@ describe('ensureDeployContext', () => {
     expect(metadataSpyOn.mock.calls[0]![0]()).toEqual({cmd_deploy_confirm_include_config_used: true})
 
     expect(renderConfirmationPrompt).toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: app.configuration.path,
-        patch: {
-          build: {include_config_on_deploy: true},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(setAppConfigValueSpy).toHaveBeenCalledWith(
+      app.configuration.path,
+      'build.include_config_on_deploy',
+      true,
+      expect.any(Object),
     )
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
@@ -228,7 +230,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('prompts the user to include the configuration and set it to false when not confirmed if the flag is not present', async () => {
@@ -243,23 +245,18 @@ describe('ensureDeployContext', () => {
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(renderConfirmationPrompt).mockResolvedValue(false)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
 
     // When
     await ensureDeployContext(deployOptions(app))
 
     // Then
     expect(renderConfirmationPrompt).toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: app.configuration.path,
-        patch: {
-          build: {include_config_on_deploy: false},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(setAppConfigValueSpy).toHaveBeenCalledWith(
+      app.configuration.path,
+      'build.include_config_on_deploy',
+      false,
+      expect.any(Object),
     )
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
@@ -277,7 +274,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('prompts the user to include the configuration if the flag is false', async () => {
@@ -295,9 +292,7 @@ describe('ensureDeployContext', () => {
     vi.mocked(link).mockResolvedValue((app as any).configuration)
     // vi.mocked(selectDeveloperPlatformClient).mockReturnValue(testDeveloperPlatformClient)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
     const metadataSpyOn = vi.spyOn(metadata, 'addPublicMetadata').mockImplementation(async () => {})
 
     const options = deployOptions(app)
@@ -310,7 +305,7 @@ describe('ensureDeployContext', () => {
     expect(metadataSpyOn).toHaveBeenCalled()
 
     expect(renderConfirmationPrompt).toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalled()
+    expect(setAppConfigValueSpy).toHaveBeenCalled()
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
         {
@@ -327,7 +322,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('doesnt prompt the user to include the configuration and display the current value if the flag is true', async () => {
@@ -345,9 +340,7 @@ describe('ensureDeployContext', () => {
     vi.mocked(link).mockResolvedValue((app as any).configuration)
     // vi.mocked(selectDeveloperPlatformClient).mockReturnValue(testDeveloperPlatformClient)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
     const metadataSpyOn = vi.spyOn(metadata, 'addPublicMetadata').mockImplementation(async () => {})
 
     const options = deployOptions(app)
@@ -360,7 +353,7 @@ describe('ensureDeployContext', () => {
     expect(metadataSpyOn).not.toHaveBeenCalled()
 
     expect(renderConfirmationPrompt).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).not.toHaveBeenCalled()
+    expect(setAppConfigValueSpy).not.toHaveBeenCalled()
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
         {
@@ -377,7 +370,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('prompts the user to include the configuration when reset is used and the flag is present', async () => {
@@ -392,9 +385,7 @@ describe('ensureDeployContext', () => {
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(renderConfirmationPrompt).mockResolvedValue(false)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
     const metadataSpyOn = vi.spyOn(metadata, 'addPublicMetadata').mockImplementation(async () => {})
 
     const options = deployOptions(app, true)
@@ -407,14 +398,11 @@ describe('ensureDeployContext', () => {
     expect(metadataSpyOn.mock.calls[0]![0]()).toEqual({cmd_deploy_confirm_include_config_used: false})
 
     expect(renderConfirmationPrompt).toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: app.configuration.path,
-        patch: {
-          build: {include_config_on_deploy: false},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(setAppConfigValueSpy).toHaveBeenCalledWith(
+      app.configuration.path,
+      'build.include_config_on_deploy',
+      false,
+      expect.any(Object),
     )
 
     expect(renderInfo).toHaveBeenCalledWith({
@@ -433,7 +421,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('doesnt prompt the user to include the configuration when force is used if the flag is not present', async () => {
@@ -448,9 +436,7 @@ describe('ensureDeployContext', () => {
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(renderConfirmationPrompt).mockResolvedValue(false)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
 
     const options = deployOptions(app, false, true)
     vi.mocked(selectDeveloperPlatformClient).mockReturnValue(options.developerPlatformClient)
@@ -460,7 +446,7 @@ describe('ensureDeployContext', () => {
 
     // Then
     expect(renderConfirmationPrompt).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).not.toHaveBeenCalled()
+    expect(setAppConfigValueSpy).not.toHaveBeenCalled()
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
         {
@@ -477,7 +463,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('prompts the user to include the configuration when force is used and the flag is present', async () => {
@@ -492,16 +478,14 @@ describe('ensureDeployContext', () => {
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(renderConfirmationPrompt).mockResolvedValue(false)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const setAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'setAppConfigValue').mockResolvedValue()
 
     // When
     await ensureDeployContext(deployOptions(app, false, true))
 
     // Then
     expect(renderConfirmationPrompt).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).not.toHaveBeenCalled()
+    expect(setAppConfigValueSpy).not.toHaveBeenCalled()
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
         {
@@ -518,7 +502,7 @@ describe('ensureDeployContext', () => {
       ],
       headline: 'Using shopify.app.toml for default values:',
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    setAppConfigValueSpy.mockRestore()
   })
 
   test('removes the include_config_on_deploy field when using app management API and the value is true', async () => {
@@ -532,9 +516,7 @@ describe('ensureDeployContext', () => {
     }
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const unsetAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'unsetAppConfigValue').mockResolvedValue()
 
     // When
     const options = {
@@ -550,14 +532,10 @@ describe('ensureDeployContext', () => {
 
     // Then
     expect(renderConfirmationPrompt).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: app.configuration.path,
-        patch: {
-          build: {include_config_on_deploy: undefined},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(unsetAppConfigValueSpy).toHaveBeenCalledWith(
+      app.configuration.path,
+      'build.include_config_on_deploy',
+      expect.any(Object),
     )
     expect(renderInfo).toHaveBeenCalledWith({
       body: [
@@ -569,7 +547,7 @@ describe('ensureDeployContext', () => {
         url: 'https://shopify.dev/docs/apps/build/cli-for-apps/app-configuration#build',
       },
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    unsetAppConfigValueSpy.mockRestore()
   })
 
   test('removes the include_config_on_deploy field when using app management API and the value is false', async () => {
@@ -583,9 +561,7 @@ describe('ensureDeployContext', () => {
     }
     vi.mocked(ensureDeploymentIdsPresence).mockResolvedValue(identifiers)
     vi.mocked(getAppConfigurationFileName).mockReturnValue('shopify.app.toml')
-    const patchAppConfigurationFileSpy = vi
-      .spyOn(patchAppConfigurationFile, 'patchAppConfigurationFile')
-      .mockResolvedValue()
+    const unsetAppConfigValueSpy = vi.spyOn(patchAppConfigurationFileModule, 'unsetAppConfigValue').mockResolvedValue()
 
     // When
     const options = {
@@ -601,14 +577,10 @@ describe('ensureDeployContext', () => {
 
     // Then
     expect(renderConfirmationPrompt).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFileSpy).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: app.configuration.path,
-        patch: {
-          build: {include_config_on_deploy: undefined},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(unsetAppConfigValueSpy).toHaveBeenCalledWith(
+      app.configuration.path,
+      'build.include_config_on_deploy',
+      expect.any(Object),
     )
     expect(renderWarning).toHaveBeenCalledWith({
       body: [
@@ -620,7 +592,7 @@ describe('ensureDeployContext', () => {
         url: 'https://shopify.dev/docs/apps/build/cli-for-apps/app-configuration#build',
       },
     })
-    patchAppConfigurationFileSpy.mockRestore()
+    unsetAppConfigValueSpy.mockRestore()
   })
 })
 
diff --git a/packages/app/src/cli/services/context.ts b/packages/app/src/cli/services/context.ts
index a42770117fc..3b11d05fd81 100644
--- a/packages/app/src/cli/services/context.ts
+++ b/packages/app/src/cli/services/context.ts
@@ -3,7 +3,7 @@ import {fetchOrganizations} from './dev/fetch.js'
 import {ensureDeploymentIdsPresence} from './context/identifiers.js'
 import {createExtension} from './dev/create-extension.js'
 import {CachedAppInfo} from './local-storage.js'
-import {patchAppConfigurationFile} from './app/patch-app-configuration-file.js'
+import {setAppConfigValue, unsetAppConfigValue} from './app/patch-app-configuration-file.js'
 import {DeployOptions} from './deploy.js'
 import {isServiceAccount, isUserAccount} from './context/partner-account-info.js'
 import {selectOrganizationPrompt} from '../prompts/dev.js'
@@ -212,8 +212,7 @@ async function removeIncludeConfigOnDeployField(localApp: AppInterface) {
   const includeConfigOnDeploy = configuration.build?.include_config_on_deploy
   if (includeConfigOnDeploy === undefined) return
 
-  const patch = {build: {include_config_on_deploy: undefined}}
-  await patchAppConfigurationFile({path: localApp.configuration.path, patch, schema: localApp.configSchema})
+  await unsetAppConfigValue(localApp.configuration.path, 'build.include_config_on_deploy', localApp.configSchema)
 
   includeConfigOnDeploy ? renderInfoAboutIncludeConfigOnDeploy() : renderWarningAboutIncludeConfigOnDeploy()
 }
@@ -251,8 +250,12 @@ async function promptIncludeConfigOnDeploy(options: ShouldOrPromptIncludeConfigD
     ...localConfiguration.build,
     include_config_on_deploy: shouldIncludeConfigDeploy,
   }
-  const patch = {build: {include_config_on_deploy: shouldIncludeConfigDeploy}}
-  await patchAppConfigurationFile({path: localConfiguration.path, patch, schema: options.localApp.configSchema})
+  await setAppConfigValue(
+    localConfiguration.path,
+    'build.include_config_on_deploy',
+    shouldIncludeConfigDeploy,
+    options.localApp.configSchema,
+  )
   await metadata.addPublicMetadata(() => ({cmd_deploy_confirm_include_config_used: shouldIncludeConfigDeploy}))
 }
 
diff --git a/packages/app/src/cli/services/dev.ts b/packages/app/src/cli/services/dev.ts
index 0da66072b93..4569fae6f24 100644
--- a/packages/app/src/cli/services/dev.ts
+++ b/packages/app/src/cli/services/dev.ts
@@ -23,7 +23,7 @@ import {DevProcessFunction} from './dev/processes/types.js'
 import {getCachedAppInfo, setCachedAppInfo} from './local-storage.js'
 import {canEnablePreviewMode} from './extensions/common.js'
 import {fetchAppRemoteConfiguration} from './app/select-app.js'
-import {patchAppConfigurationFile} from './app/patch-app-configuration-file.js'
+import {setManyAppConfigValues} from './app/patch-app-configuration-file.js'
 import {DevSessionStatusManager} from './dev/processes/dev-session/dev-session-status-manager.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
 import {Web, isCurrentAppSchema, getAppScopesArray, AppLinkedInterface} from '../models/app/app.js'
@@ -124,8 +124,11 @@ async function prepareForDev(commandOptions: DevOptions): Promise<DevConfig> {
       ...app.configuration.build,
       dev_store_url: store.shopDomain,
     }
-    const patch = {build: {dev_store_url: store.shopDomain}}
-    await patchAppConfigurationFile({path: app.configuration.path, patch, schema: app.configSchema})
+    await setManyAppConfigValues(
+      app.configuration.path,
+      [{keyPath: 'build.dev_store_url', value: store.shopDomain}],
+      app.configSchema,
+    )
   }
 
   if (!commandOptions.skipDependenciesInstallation && !app.usesWorkspaces) {
@@ -246,7 +249,7 @@ export async function warnIfScopesDifferBeforeDev({
 }
 
 async function actionsBeforeLaunchingDevProcesses(config: DevConfig) {
-  setPreviousAppId(config.commandOptions.directory, config.remoteApp.apiKey)
+  setCachedAppInfo({directory: config.commandOptions.directory, previousAppId: config.remoteApp.apiKey})
 
   await logMetadataForDev({
     devOptions: config.commandOptions,
@@ -520,7 +523,3 @@ async function validateCustomPorts(webConfigs: Web[], graphiqlPort: number) {
     })(),
   ])
 }
-
-function setPreviousAppId(directory: string, apiKey: string) {
-  setCachedAppInfo({directory, previousAppId: apiKey})
-}
diff --git a/packages/app/src/cli/services/dev/urls.test.ts b/packages/app/src/cli/services/dev/urls.test.ts
index fb7505ffd23..e9b65bcef15 100644
--- a/packages/app/src/cli/services/dev/urls.test.ts
+++ b/packages/app/src/cli/services/dev/urls.test.ts
@@ -15,7 +15,7 @@ import {
 } from '../../models/app/app.test-data.js'
 import {UpdateURLsVariables} from '../../api/graphql/update_urls.js'
 import {setCachedAppInfo} from '../local-storage.js'
-import {patchAppConfigurationFile} from '../app/patch-app-configuration-file.js'
+import {setManyAppConfigValues} from '../app/patch-app-configuration-file.js'
 import {AppLinkedInterface} from '../../models/app/app.js'
 import {beforeEach, describe, expect, vi, test} from 'vitest'
 import {AbortError} from '@shopify/cli-kit/node/error'
@@ -26,7 +26,11 @@ import {renderConfirmationPrompt, renderSelectPrompt} from '@shopify/cli-kit/nod
 import {terminalSupportsPrompting} from '@shopify/cli-kit/node/system'
 
 vi.mock('../local-storage.js')
-vi.mock('../app/patch-app-configuration-file.js')
+vi.mock('../app/patch-app-configuration-file.js', () => {
+  return {
+    setManyAppConfigValues: vi.fn(),
+  }
+})
 vi.mock('@shopify/cli-kit/node/tcp')
 vi.mock('@shopify/cli-kit/node/context/spin')
 vi.mock('@shopify/cli-kit/node/context/local')
@@ -92,21 +96,20 @@ describe('updateURLs', () => {
     await updateURLs(urls, apiKey, testDeveloperPlatformClient(), appWithConfig)
 
     // Then
-    expect(patchAppConfigurationFile).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: appWithConfig.configuration.path,
-        patch: {
-          application_url: 'https://example.com',
-          auth: {
-            redirect_urls: [
-              'https://example.com/auth/callback',
-              'https://example.com/auth/shopify/callback',
-              'https://example.com/api/auth/callback',
-            ],
-          },
+    expect(setManyAppConfigValues).toHaveBeenCalledWith(
+      appWithConfig.configuration.path,
+      [
+        {keyPath: 'application_url', value: 'https://example.com'},
+        {
+          keyPath: 'auth.redirect_urls',
+          value: [
+            'https://example.com/auth/callback',
+            'https://example.com/auth/shopify/callback',
+            'https://example.com/api/auth/callback',
+          ],
         },
-        schema: expect.any(Object),
-      }),
+      ],
+      expect.any(Object),
     )
   })
 
@@ -180,26 +183,23 @@ describe('updateURLs', () => {
     await updateURLs(urls, apiKey, testDeveloperPlatformClient(), appWithConfig)
 
     // Then
-    expect(patchAppConfigurationFile).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: appWithConfig.configuration.path,
-        patch: {
-          application_url: 'https://example.com',
-          auth: {
-            redirect_urls: [
-              'https://example.com/auth/callback',
-              'https://example.com/auth/shopify/callback',
-              'https://example.com/api/auth/callback',
-            ],
-          },
-          app_proxy: {
-            url: 'https://example.com',
-            subpath: 'subpath',
-            prefix: 'prefix',
-          },
+    expect(setManyAppConfigValues).toHaveBeenCalledWith(
+      appWithConfig.configuration.path,
+      [
+        {keyPath: 'application_url', value: 'https://example.com'},
+        {
+          keyPath: 'auth.redirect_urls',
+          value: [
+            'https://example.com/auth/callback',
+            'https://example.com/auth/shopify/callback',
+            'https://example.com/api/auth/callback',
+          ],
         },
-        schema: expect.any(Object),
-      }),
+        {keyPath: 'app_proxy.url', value: 'https://example.com'},
+        {keyPath: 'app_proxy.subpath', value: 'subpath'},
+        {keyPath: 'app_proxy.prefix', value: 'prefix'},
+      ],
+      expect.any(Object),
     )
   })
 })
@@ -360,7 +360,7 @@ describe('shouldOrPromptUpdateURLs', () => {
     // Then
     expect(result).toBe(true)
     expect(setCachedAppInfo).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFile).not.toHaveBeenCalled()
+    expect(setManyAppConfigValues).not.toHaveBeenCalled()
   })
 
   test('updates the config file if current config client matches remote', async () => {
@@ -385,14 +385,10 @@ describe('shouldOrPromptUpdateURLs', () => {
     // Then
     expect(result).toBe(true)
     expect(setCachedAppInfo).not.toHaveBeenCalled()
-    expect(patchAppConfigurationFile).toHaveBeenCalledWith(
-      expect.objectContaining({
-        path: localApp.configuration.path,
-        patch: {
-          build: {automatically_update_urls_on_dev: true},
-        },
-        schema: expect.any(Object),
-      }),
+    expect(setManyAppConfigValues).toHaveBeenCalledWith(
+      localApp.configuration.path,
+      [{keyPath: 'build.automatically_update_urls_on_dev', value: true}],
+      localApp.configSchema,
     )
   })
 })
diff --git a/packages/app/src/cli/services/dev/urls.ts b/packages/app/src/cli/services/dev/urls.ts
index 8567869ed2b..53c313f117f 100644
--- a/packages/app/src/cli/services/dev/urls.ts
+++ b/packages/app/src/cli/services/dev/urls.ts
@@ -4,7 +4,7 @@ import {UpdateURLsSchema, UpdateURLsVariables} from '../../api/graphql/update_ur
 import {setCachedAppInfo} from '../local-storage.js'
 import {AppConfigurationUsedByCli} from '../../models/extensions/specifications/types/app_config.js'
 import {DeveloperPlatformClient} from '../../utilities/developer-platform-client.js'
-import {patchAppConfigurationFile} from '../app/patch-app-configuration-file.js'
+import {setManyAppConfigValues} from '../app/patch-app-configuration-file.js'
 import {AbortError, BugError} from '@shopify/cli-kit/node/error'
 import {Config} from '@oclif/core'
 import {checkPortAvailability, getAvailableTCPPort} from '@shopify/cli-kit/node/tcp'
@@ -197,23 +197,20 @@ export async function updateURLs(
   }
 
   if (localApp && localApp.configuration.client_id === apiKey) {
-    const patch = {
-      application_url: urls.applicationUrl,
-      auth: {
-        redirect_urls: urls.redirectUrlWhitelist,
-      },
-      ...(urls.appProxy
-        ? {
-            app_proxy: {
-              url: urls.appProxy.proxyUrl,
-              subpath: urls.appProxy.proxySubPath,
-              prefix: urls.appProxy.proxySubPathPrefix,
-            },
-          }
-        : {}),
+    const configValues = [
+      {keyPath: 'application_url', value: urls.applicationUrl},
+      {keyPath: 'auth.redirect_urls', value: urls.redirectUrlWhitelist},
+    ]
+
+    if (urls.appProxy) {
+      configValues.push(
+        {keyPath: 'app_proxy.url', value: urls.appProxy.proxyUrl},
+        {keyPath: 'app_proxy.subpath', value: urls.appProxy.proxySubPath},
+        {keyPath: 'app_proxy.prefix', value: urls.appProxy.proxySubPathPrefix},
+      )
     }
 
-    await patchAppConfigurationFile({path: localApp.configuration.path, patch, schema: localApp.configSchema})
+    await setManyAppConfigValues(localApp.configuration.path, configValues, localApp.configSchema)
   }
 }
 
@@ -262,9 +259,12 @@ export async function shouldOrPromptUpdateURLs(options: ShouldOrPromptUpdateURLs
         ...localConfiguration.build,
         automatically_update_urls_on_dev: shouldUpdateURLs,
       }
-      const patch = {build: {automatically_update_urls_on_dev: shouldUpdateURLs}}
       const path = options.localApp.configuration.path
-      await patchAppConfigurationFile({path, patch, schema: options.localApp.configSchema})
+      await setManyAppConfigValues(
+        path,
+        [{keyPath: 'build.automatically_update_urls_on_dev', value: shouldUpdateURLs}],
+        options.localApp.configSchema,
+      )
     } else {
       setCachedAppInfo({directory: options.appDirectory, updateURLs: shouldUpdateURLs})
     }