diff --git a/src/Console/AddSkillCommand.php b/src/Console/AddSkillCommand.php
index 9a3b1134..c140b38b 100644
--- a/src/Console/AddSkillCommand.php
+++ b/src/Console/AddSkillCommand.php
@@ -16,6 +16,7 @@
 use Laravel\Boost\Skills\Remote\GitHubSkillProvider;
 use Laravel\Boost\Skills\Remote\RemoteSkill;
 use Laravel\Boost\Skills\Remote\SkillAuditor;
+use Laravel\Boost\Support\Config;
 use Laravel\Prompts\Terminal;
 use RuntimeException;
 
@@ -52,8 +53,10 @@ class AddSkillCommand extends Command
 
     protected string $defaultSkillsPath = '.ai/skills';
 
-    public function __construct(private readonly Terminal $terminal)
-    {
+    public function __construct(
+        private readonly Terminal $terminal,
+        private readonly Config $config,
+    ) {
         parent::__construct();
     }
 
@@ -287,6 +290,7 @@ protected function downloadSkills(Collection $skills): array
     protected function addSkills(Collection $skills): array
     {
         $results = ['installedNames' => [], 'failedDetails' => []];
+        $skillsToTrack = [];
 
         foreach ($skills as $skill) {
             $targetPath = $this->skillTargetPath($skill);
@@ -298,6 +302,14 @@ protected function addSkills(Collection $skills): array
             try {
                 if ($this->fetcher->downloadSkill($skill, $targetPath)) {
                     $results['installedNames'][] = $skill->name;
+                    $skillsToTrack[$skill->name] = [
+                        'source' => Config::SKILL_SOURCE_GITHUB,
+                        'repo' => $skill->repo,
+                    ];
+
+                    if ($skill->path !== $skill->name) {
+                        $skillsToTrack[$skill->name]['path'] = $skill->path;
+                    }
                 } else {
                     $results['failedDetails'][$skill->name] = 'Download failed';
                 }
@@ -306,6 +318,10 @@ protected function addSkills(Collection $skills): array
             }
         }
 
+        if ($skillsToTrack !== []) {
+            $this->config->trackSkills($skillsToTrack);
+        }
+
         return $results;
     }
 
diff --git a/src/Console/InstallCommand.php b/src/Console/InstallCommand.php
index ceb7058b..130288c1 100644
--- a/src/Console/InstallCommand.php
+++ b/src/Console/InstallCommand.php
@@ -66,6 +66,9 @@ class InstallCommand extends Command
     /** @var array<int, string> */
     private array $installedSkillNames = [];
 
+    /** @var array<string, array<string, string>> */
+    private array $installedSkillMetadata = [];
+
     const MIN_TEST_COUNT = 6;
 
     public function __construct(
@@ -365,6 +368,13 @@ protected function installSkills(): void
         $skills = $skillsComposer->skills();
 
         $this->installedSkillNames = $skills->keys()->toArray();
+        $this->installedSkillMetadata = $skills
+            ->mapWithKeys(fn (Skill $skill): array => [
+                $skill->name => [
+                    'source' => $skill->custom ? Config::SKILL_SOURCE_CUSTOM : Config::SKILL_SOURCE_OFFICIAL,
+                ],
+            ])
+            ->all();
 
         /** @var Collection<int, SupportsSkills&Agent> $skillsAgents */
         $this->installFeature(
@@ -433,7 +443,7 @@ protected function storeConfig(): void
         }
 
         if ($this->selectedBoostFeatures->contains('skills')) {
-            $this->config->setSkills($this->installedSkillNames);
+            $this->config->setSkills($this->installedSkillNames, $this->installedSkillMetadata);
         }
 
         $this->config->setCloud($this->selectedBoostFeatures->contains('cloud'));
diff --git a/src/Support/Config.php b/src/Support/Config.php
index f8613e31..374ca4e7 100644
--- a/src/Support/Config.php
+++ b/src/Support/Config.php
@@ -10,6 +10,14 @@ class Config
 {
     protected const FILE = 'boost.json';
 
+    public const SKILL_SOURCE_CUSTOM = 'custom';
+
+    public const SKILL_SOURCE_GITHUB = 'github';
+
+    public const SKILL_SOURCE_OFFICIAL = 'official';
+
+    protected const LEGACY_OFFICIAL_SKILLS_SOURCE = 'laravel/boost';
+
     public function getGuidelines(): bool
     {
         return (bool) $this->get('guidelines', false);
@@ -25,15 +33,31 @@ public function setGuidelines(bool $enabled): void
      */
     public function getSkills(): array
     {
-        return $this->get('skills', []);
+        return array_keys($this->getSkillMetadata());
     }
 
     /**
      * @param  array<int, string>  $skills
+     * @param  array<string, array<string, string>>  $metadata
      */
-    public function setSkills(array $skills): void
+    public function setSkills(array $skills, array $metadata = []): void
     {
-        $this->set('skills', $skills);
+        $currentMetadata = $this->getSkillMetadata();
+        $selectedSkills = [];
+
+        foreach ($skills as $skillName) {
+            if ($skillName === '') {
+                continue;
+            }
+
+            $selectedSkills[$skillName] = $this->resolveSkillMetadata(
+                skillName: $skillName,
+                currentMetadata: $currentMetadata[$skillName] ?? [],
+                incomingMetadata: $metadata[$skillName] ?? $currentMetadata[$skillName] ?? ['source' => self::SKILL_SOURCE_OFFICIAL],
+            );
+        }
+
+        $this->set('skills', $this->sortSkillsByName($selectedSkills));
     }
 
     public function hasSkills(): bool
@@ -41,6 +65,206 @@ public function hasSkills(): bool
         return $this->getSkills() !== [];
     }
 
+    /**
+     * @return array<string, array<string, string>>
+     */
+    public function getTrackedSkills(): array
+    {
+        return $this->getSkillMetadata();
+    }
+
+    /**
+     * @return array<string, array<string, string>>
+     */
+    public function getSkillMetadata(): array
+    {
+        return $this->extractSkillMetadata($this->getRawSkills());
+    }
+
+    /**
+     * @param  array<string, array<string, string>|string>  $skills
+     */
+    public function trackSkills(array $skills): void
+    {
+        $metadata = $this->getSkillMetadata();
+
+        foreach ($skills as $skillName => $skillMetadata) {
+            if ($skillName === '') {
+                continue;
+            }
+
+            $metadata[$skillName] = $this->normalizeSkillMetadata($skillName, $skillMetadata);
+        }
+
+        $this->set('skills', $this->sortSkillsByName($metadata));
+    }
+
+    public function trackSkill(string $skillName, string $source): void
+    {
+        $this->trackSkills([$skillName => $source]);
+    }
+
+    protected function extractSkillMetadata(array $currentConfig): array
+    {
+        if (array_is_list($currentConfig)) {
+            $metadata = [];
+
+            foreach ($currentConfig as $value) {
+                if (is_string($value) && $value !== '') {
+                    $metadata[$value] = ['source' => self::SKILL_SOURCE_CUSTOM];
+                }
+            }
+
+            return $metadata;
+        }
+
+        $metadata = [];
+
+        foreach ($currentConfig as $key => $value) {
+            if (is_array($value) && array_is_list($value)) {
+                $source = is_string($key) && $key !== '' ? $key : self::SKILL_SOURCE_CUSTOM;
+
+                foreach ($value as $skillName) {
+                    if (is_string($skillName) && $skillName !== '') {
+                        $metadata[$skillName] = $this->metadataFromLegacySource($skillName, $source);
+                    }
+                }
+
+                continue;
+            }
+
+            if (! is_string($key) || $key === '') {
+                continue;
+            }
+
+            if (is_bool($value)) {
+                $metadata[$key] = ['source' => $value ? self::SKILL_SOURCE_OFFICIAL : self::SKILL_SOURCE_CUSTOM];
+
+                continue;
+            }
+
+            if (is_string($value)) {
+                $metadata[$key] = $this->metadataFromLegacySource($key, $value);
+
+                continue;
+            }
+
+            if (is_array($value)) {
+                $metadata[$key] = $this->normalizeSkillMetadata($key, $value);
+            }
+        }
+
+        return $metadata;
+    }
+
+    /**
+     * @param  array<string, mixed>|string  $metadata
+     * @return array<string, string>
+     */
+    protected function normalizeSkillMetadata(string $skillName, array|string $metadata): array
+    {
+        if (is_string($metadata)) {
+            return $this->metadataFromLegacySource($skillName, $metadata);
+        }
+
+        $source = $metadata['source'] ?? self::SKILL_SOURCE_CUSTOM;
+
+        if (! is_string($source) || $source === '') {
+            return ['source' => self::SKILL_SOURCE_CUSTOM];
+        }
+
+        if ($source === self::SKILL_SOURCE_GITHUB) {
+            return $this->githubMetadata(
+                skillName: $skillName,
+                repo: $metadata['repo'] ?? null,
+                path: $metadata['path'] ?? null,
+            );
+        }
+
+        return $this->metadataFromLegacySource($skillName, $source);
+    }
+
+    /**
+     * @return array<string, string>
+     */
+    protected function metadataFromLegacySource(string $skillName, string $source): array
+    {
+        $source = trim($source, '/');
+
+        if ($source === '' || $source === self::SKILL_SOURCE_CUSTOM) {
+            return ['source' => self::SKILL_SOURCE_CUSTOM];
+        }
+
+        if ($source === self::SKILL_SOURCE_OFFICIAL || $source === self::LEGACY_OFFICIAL_SKILLS_SOURCE) {
+            return ['source' => self::SKILL_SOURCE_OFFICIAL];
+        }
+
+        $parts = explode('/', $source);
+
+        if (count($parts) < 2 || $parts[0] === '' || $parts[1] === '') {
+            return ['source' => self::SKILL_SOURCE_CUSTOM];
+        }
+
+        $repo = $parts[0].'/'.$parts[1];
+        $basePath = implode('/', array_slice($parts, 2));
+        $path = $basePath === '' ? $skillName : $basePath.'/'.$skillName;
+
+        return $this->githubMetadata($skillName, $repo, $path);
+    }
+
+    /**
+     * @return array<string, string>
+     */
+    protected function githubMetadata(string $skillName, mixed $repo, mixed $path = null): array
+    {
+        if (! is_string($repo) || $repo === '') {
+            return ['source' => self::SKILL_SOURCE_CUSTOM];
+        }
+
+        $metadata = [
+            'source' => self::SKILL_SOURCE_GITHUB,
+            'repo' => $repo,
+        ];
+
+        if (is_string($path) && $path !== '' && $path !== $skillName) {
+            $metadata['path'] = $path;
+        }
+
+        return $metadata;
+    }
+
+    /**
+     * @param  array<string, string>  $currentMetadata
+     * @param  array<string, string>  $incomingMetadata
+     * @return array<string, string>
+     */
+    protected function resolveSkillMetadata(string $skillName, array $currentMetadata, array $incomingMetadata): array
+    {
+        $currentMetadata = $this->normalizeSkillMetadata($skillName, $currentMetadata);
+        $incomingMetadata = $this->normalizeSkillMetadata($skillName, $incomingMetadata);
+
+        $currentSource = $currentMetadata['source'] ?? null;
+        $incomingSource = $incomingMetadata['source'] ?? null;
+
+        // Preserve existing GitHub metadata when the incoming entry only carries the default custom source.
+        if ($currentSource === self::SKILL_SOURCE_GITHUB && $incomingSource === self::SKILL_SOURCE_CUSTOM) {
+            return $currentMetadata;
+        }
+
+        return $incomingMetadata;
+    }
+
+    /**
+     * @param  array<string, array<string, string>>  $metadata
+     * @return array<string, array<string, string>>
+     */
+    protected function sortSkillsByName(array $metadata): array
+    {
+        ksort($metadata);
+
+        return $metadata;
+    }
+
     public function getMcp(): bool
     {
         return $this->get('mcp', false);
@@ -135,6 +359,13 @@ public function flush(): void
         }
     }
 
+    protected function getRawSkills(): array
+    {
+        $skills = $this->get('skills', []);
+
+        return is_array($skills) ? $skills : [];
+    }
+
     protected function get(string $key, mixed $default = null): mixed
     {
         $config = $this->all();
diff --git a/tests/Feature/Console/AddSkillCommandTest.php b/tests/Feature/Console/AddSkillCommandTest.php
index cb60e859..aff50b8a 100644
--- a/tests/Feature/Console/AddSkillCommandTest.php
+++ b/tests/Feature/Console/AddSkillCommandTest.php
@@ -4,12 +4,14 @@
 
 use Illuminate\Support\Facades\File;
 use Illuminate\Support\Facades\Http;
+use Laravel\Boost\Support\Config;
 use Orchestra\Testbench\Concerns\InteractsWithPublishedFiles;
 
 uses(InteractsWithPublishedFiles::class);
 
 beforeEach(function (): void {
     File::deleteDirectory(base_path('.ai/skills'));
+    (new Config)->flush();
 
     $this->files = [
         '.ai/skills/skill-one/SKILL.md',
@@ -93,6 +95,48 @@
 
     $this->assertFilenameExists('.ai/skills/skill-one/SKILL.md');
     $this->assertFileContains(['# SKILL Content'], '.ai/skills/skill-one/SKILL.md');
+
+    $config = json_decode((string) file_get_contents(base_path('boost.json')), true);
+
+    expect($config['skills']['skill-one'])->toBe([
+        'source' => 'github',
+        'repo' => 'owner/repo',
+    ]);
+});
+
+it('tracks installed skills in boost json using source metadata', function (): void {
+    Http::fake([
+        'api.github.com/repos/owner/repo/git/trees/main?recursive=1' => Http::response([
+            'sha' => 'repo-tree-sha',
+            'tree' => [
+                ['path' => 'path/to/skills/skill-one', 'type' => 'tree', 'sha' => 'skill-one-tree-sha'],
+                ['path' => 'path/to/skills/skill-one/SKILL.md', 'type' => 'blob', 'sha' => 'skill-file-sha', 'size' => 123],
+            ],
+            'truncated' => false,
+        ]),
+        'raw.githubusercontent.com/*' => Http::response(<<<'YAML'
+            ---
+            name: skill-one
+            description: First skill
+            ---
+            # SKILL Content
+            YAML),
+    ]);
+
+    $this->artisan('boost:add-skill', [
+        'repo' => 'owner/repo/path/to/skills',
+        '--all' => true,
+    ])->assertSuccessful();
+
+    $config = json_decode((string) file_get_contents(base_path('boost.json')), true);
+
+    expect($config['skills'])->toBe([
+        'skill-one' => [
+            'source' => 'github',
+            'repo' => 'owner/repo',
+            'path' => 'path/to/skills/skill-one',
+        ],
+    ]);
 });
 
 it('installs specific skills with --skill option', function (): void {
diff --git a/tests/Unit/Skills/Remote/GitHubSkillProviderTest.php b/tests/Unit/Skills/Remote/GitHubSkillProviderTest.php
index 850b8b83..de0eb7ea 100644
--- a/tests/Unit/Skills/Remote/GitHubSkillProviderTest.php
+++ b/tests/Unit/Skills/Remote/GitHubSkillProviderTest.php
@@ -11,7 +11,6 @@
 beforeEach(function (): void {
     Http::preventStrayRequests();
 });
-
 function fakeGitHubRepo(string $branch = 'main'): array
 {
     return ['api.github.com/repos/owner/repo' => Http::response(['default_branch' => $branch])];
diff --git a/tests/Unit/Support/ConfigTest.php b/tests/Unit/Support/ConfigTest.php
index bf11844e..d4947622 100644
--- a/tests/Unit/Support/ConfigTest.php
+++ b/tests/Unit/Support/ConfigTest.php
@@ -2,6 +2,10 @@
 
 use Laravel\Boost\Support\Config;
 
+beforeEach(function (): void {
+    (new Config)->flush();
+});
+
 afterEach(function (): void {
     (new Config)->flush();
 });
@@ -49,7 +53,11 @@
     $config->setSkills($skills);
 
     expect($config->getSkills())->toEqual($skills)
-        ->and($config->hasSkills())->toBeTrue();
+        ->and($config->hasSkills())->toBeTrue()
+        ->and($config->getSkillMetadata())->toBe([
+            'skill-one' => ['source' => 'official'],
+            'skill-two' => ['source' => 'official'],
+        ]);
 
     $config->setSkills([]);
 
@@ -101,3 +109,118 @@
 
     expect($config->getPackages())->toEqual($packages);
 });
+
+it('may track and query skills with source metadata', function (): void {
+    $config = new Config;
+
+    expect($config->getTrackedSkills())->toBeEmpty();
+
+    $config->trackSkills([
+        'composition-patterns' => [
+            'source' => 'github',
+            'repo' => 'vercel-labs/agent-skills',
+        ],
+        'algorithmic-art' => [
+            'source' => 'github',
+            'repo' => 'anthropics/skills',
+        ],
+    ]);
+
+    $tracked = $config->getTrackedSkills();
+
+    expect($tracked)->toHaveKeys(['composition-patterns', 'algorithmic-art'])
+        ->and($tracked['composition-patterns'])->toBe([
+            'source' => 'github',
+            'repo' => 'vercel-labs/agent-skills',
+        ])
+        ->and($tracked['algorithmic-art'])->toBe([
+            'source' => 'github',
+            'repo' => 'anthropics/skills',
+        ]);
+});
+
+it('keeps tracked source metadata when syncing skills list', function (): void {
+    $config = new Config;
+
+    $config->setSkills(['algorithmic-art']);
+    $config->trackSkills([
+        'algorithmic-art' => [
+            'source' => 'github',
+            'repo' => 'anthropics/skills',
+        ],
+    ]);
+    $config->setSkills(['algorithmic-art', 'pest-testing'], [
+        'algorithmic-art' => ['source' => 'custom'],
+        'pest-testing' => ['source' => 'official'],
+    ]);
+
+    expect($config->getSkills())->toBe(['algorithmic-art', 'pest-testing']);
+
+    $tracked = $config->getTrackedSkills();
+
+    expect($tracked['algorithmic-art'])->toBe([
+        'source' => 'github',
+        'repo' => 'anthropics/skills',
+    ])->and($tracked['pest-testing'])->toBe(['source' => 'official']);
+});
+
+it('normalizes legacy list-format skills into skill metadata format', function (): void {
+    file_put_contents(base_path('boost.json'), json_encode([
+        'agents' => ['claude_code'],
+        'skills' => ['pest-testing', 'fortify-development'],
+    ], JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES));
+
+    $config = new Config;
+
+    expect($config->getSkills())->toBe(['pest-testing', 'fortify-development']);
+
+    $config->setSkills($config->getSkills());
+
+    $normalized = json_decode((string) file_get_contents(base_path('boost.json')), true);
+
+    expect($normalized['skills'])->toBe([
+        'fortify-development' => ['source' => 'custom'],
+        'pest-testing' => ['source' => 'custom'],
+    ]);
+});
+
+it('reads legacy flat-format skill source metadata', function (): void {
+    file_put_contents(base_path('boost.json'), json_encode([
+        'agents' => ['claude_code'],
+        'skills' => [
+            'copilot-docs' => ['source' => 'anthropics/skills'],
+            'pest-testing' => ['source' => ''],
+        ],
+    ], JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES));
+
+    $config = new Config;
+    $tracked = $config->getTrackedSkills();
+
+    expect($config->getSkills())->toBe(['copilot-docs', 'pest-testing'])
+        ->and($tracked['copilot-docs'])->toBe([
+            'source' => 'github',
+            'repo' => 'anthropics/skills',
+        ])
+        ->and($tracked['pest-testing'])->toBe(['source' => 'custom']);
+});
+
+it('reads legacy grouped source metadata', function (): void {
+    file_put_contents(base_path('boost.json'), json_encode([
+        'agents' => ['claude_code'],
+        'skills' => [
+            'laravel/boost' => ['pest-testing'],
+            'owner/repo/path/to/skills' => ['skill-one'],
+        ],
+    ], JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES));
+
+    $config = new Config;
+
+    expect($config->getSkillMetadata())->toBe([
+        'pest-testing' => ['source' => 'official'],
+        'skill-one' => [
+            'source' => 'github',
+            'repo' => 'owner/repo',
+            'path' => 'path/to/skills/skill-one',
+        ],
+    ]);
+});