diff --git a/.changeset/orange-geckos-cross.md b/.changeset/orange-geckos-cross.md
new file mode 100644
index 0000000..ab91c06
--- /dev/null
+++ b/.changeset/orange-geckos-cross.md
@@ -0,0 +1,5 @@
+---
+"@swc/cli": patch
+---
+
+fix(cli): Clone config instead of updating it
diff --git a/packages/cli/src/swc/dir.ts b/packages/cli/src/swc/dir.ts
index 78733ca..f39b565 100644
--- a/packages/cli/src/swc/dir.ts
+++ b/packages/cli/src/swc/dir.ts
@@ -401,12 +401,20 @@ export default async function dir({
     swcOptions: Options;
     callbacks?: Callbacks;
 }) {
-    const { watch } = cliOptions;
+    // Deep clone the configuration objects to prevent reuse between calls
+    const clonedCliOptions = JSON.parse(JSON.stringify(cliOptions));
+    const clonedSwcOptions = JSON.parse(JSON.stringify(swcOptions));
 
-    await beforeStartCompilation(cliOptions);
-    await initialCompilation(cliOptions, swcOptions, callbacks);
+    await beforeStartCompilation(clonedCliOptions);
 
-    if (watch) {
-        await watchCompilation(cliOptions, swcOptions, callbacks);
+    await initialCompilation(clonedCliOptions, clonedSwcOptions, callbacks);
+
+    if (clonedCliOptions.watch) {
+        const watcher = await watchCompilation(
+            clonedCliOptions,
+            clonedSwcOptions,
+            callbacks
+        );
+        return watcher;
     }
 }
diff --git a/packages/cli/src/swc/dirWorker.ts b/packages/cli/src/swc/dirWorker.ts
index 53c6673..916c0c3 100644
--- a/packages/cli/src/swc/dirWorker.ts
+++ b/packages/cli/src/swc/dirWorker.ts
@@ -23,7 +23,10 @@ export default async function handleCompile(opts: {
     );
     const sourceFileName = slash(relative(dirname(dest), opts.filename));
 
-    const options = { ...opts.swcOptions, sourceFileName };
+    // Create a deep copy of the options to prevent mutation affecting other compilations
+    const options = JSON.parse(
+        JSON.stringify({ ...opts.swcOptions, sourceFileName })
+    );
 
     const result = await compile(opts.filename, options, opts.sync, dest);