diff --git a/app/Models/Team.php b/app/Models/Team.php
index 8a54a9dee..d5d564444 100644
--- a/app/Models/Team.php
+++ b/app/Models/Team.php
@@ -71,25 +71,31 @@ protected static function booted()
             }
         });
 
-        static::deleting(function ($team) {
-            $keys = $team->privateKeys;
-            foreach ($keys as $key) {
+        static::deleting(function (Team $team) {
+            foreach ($team->privateKeys as $key) {
                 $key->delete();
             }
-            $sources = $team->sources();
-            foreach ($sources as $source) {
+
+            // Transfer instance-wide sources to root team so they remain available
+            GithubApp::where('team_id', $team->id)->where('is_system_wide', true)->update(['team_id' => 0]);
+            GitlabApp::where('team_id', $team->id)->where('is_system_wide', true)->update(['team_id' => 0]);
+
+            // Delete non-instance-wide sources owned by this team
+            $teamSources = GithubApp::where('team_id', $team->id)->get()
+                ->merge(GitlabApp::where('team_id', $team->id)->get());
+            foreach ($teamSources as $source) {
                 $source->delete();
             }
-            $tags = Tag::whereTeamId($team->id)->get();
-            foreach ($tags as $tag) {
+
+            foreach (Tag::whereTeamId($team->id)->get() as $tag) {
                 $tag->delete();
             }
-            $shared_variables = $team->environment_variables();
-            foreach ($shared_variables as $shared_variable) {
-                $shared_variable->delete();
+
+            foreach ($team->environment_variables()->get() as $sharedVariable) {
+                $sharedVariable->delete();
             }
-            $s3s = $team->s3s;
-            foreach ($s3s as $s3) {
+
+            foreach ($team->s3s as $s3) {
                 $s3->delete();
             }
         });
@@ -338,4 +344,5 @@ public function webhookNotificationSettings()
     {
         return $this->hasOne(WebhookNotificationSettings::class);
     }
+
 }
diff --git a/tests/Feature/UserDeletionWithGithubAppTest.php b/tests/Feature/UserDeletionWithGithubAppTest.php
new file mode 100644
index 000000000..b2ccbccb0
--- /dev/null
+++ b/tests/Feature/UserDeletionWithGithubAppTest.php
@@ -0,0 +1,218 @@
+<?php
+
+use App\Models\Application;
+use App\Models\Environment;
+use App\Models\GithubApp;
+use App\Models\PrivateKey;
+use App\Models\Project;
+use App\Models\Server;
+use App\Models\StandaloneDocker;
+use App\Models\Team;
+use App\Models\User;
+use Illuminate\Foundation\Testing\RefreshDatabase;
+
+uses(RefreshDatabase::class);
+
+beforeEach(function () {
+    // Create root team and admin user (instance admin)
+    $this->rootTeam = Team::factory()->create(['id' => 0, 'name' => 'Root Team']);
+    $this->adminUser = User::factory()->create();
+    $this->rootTeam->members()->attach($this->adminUser->id, ['role' => 'owner']);
+    $this->actingAs($this->adminUser);
+    session(['currentTeam' => $this->rootTeam]);
+});
+
+it('deletes a user whose team has a github app with applications', function () {
+    // Create the user to be deleted with their own team
+    $targetUser = User::factory()->create();
+    $targetTeam = $targetUser->teams()->first(); // created by User::created event
+
+    // Create a private key for the team
+    $privateKey = PrivateKey::factory()->create(['team_id' => $targetTeam->id]);
+
+    // Create a server and destination for the team
+    $server = Server::factory()->create([
+        'team_id' => $targetTeam->id,
+        'private_key_id' => $privateKey->id,
+    ]);
+    $destination = StandaloneDocker::factory()->create(['server_id' => $server->id]);
+
+    // Create a project and environment
+    $project = Project::factory()->create(['team_id' => $targetTeam->id]);
+    $environment = Environment::factory()->create(['project_id' => $project->id]);
+
+    // Create a GitHub App owned by the target team
+    $githubApp = GithubApp::create([
+        'name' => 'Test GitHub App',
+        'team_id' => $targetTeam->id,
+        'private_key_id' => $privateKey->id,
+        'api_url' => 'https://api.github.com',
+        'html_url' => 'https://github.com',
+        'is_public' => false,
+    ]);
+
+    // Create an application that uses the GitHub App as its source
+    $application = Application::factory()->create([
+        'environment_id' => $environment->id,
+        'destination_id' => $destination->id,
+        'destination_type' => StandaloneDocker::class,
+        'source_id' => $githubApp->id,
+        'source_type' => GithubApp::class,
+    ]);
+
+    // Delete the user — this should NOT throw a GithubApp exception
+    $targetUser->delete();
+
+    // Assert user is deleted
+    expect(User::find($targetUser->id))->toBeNull();
+
+    // Assert the GitHub App is deleted
+    expect(GithubApp::find($githubApp->id))->toBeNull();
+
+    // Assert the application is deleted
+    expect(Application::find($application->id))->toBeNull();
+});
+
+it('does not delete system-wide github apps when deleting a different team', function () {
+    // Create a system-wide GitHub App owned by the root team
+    $rootPrivateKey = PrivateKey::factory()->create(['team_id' => $this->rootTeam->id]);
+    $systemGithubApp = GithubApp::create([
+        'name' => 'System GitHub App',
+        'team_id' => $this->rootTeam->id,
+        'private_key_id' => $rootPrivateKey->id,
+        'api_url' => 'https://api.github.com',
+        'html_url' => 'https://github.com',
+        'is_public' => false,
+        'is_system_wide' => true,
+    ]);
+
+    // Create a target user with their own team
+    $targetUser = User::factory()->create();
+    $targetTeam = $targetUser->teams()->first();
+
+    // Create an application on the target team that uses the system-wide GitHub App
+    $privateKey = PrivateKey::factory()->create(['team_id' => $targetTeam->id]);
+    $server = Server::factory()->create([
+        'team_id' => $targetTeam->id,
+        'private_key_id' => $privateKey->id,
+    ]);
+    $destination = StandaloneDocker::factory()->create(['server_id' => $server->id]);
+    $project = Project::factory()->create(['team_id' => $targetTeam->id]);
+    $environment = Environment::factory()->create(['project_id' => $project->id]);
+
+    $application = Application::factory()->create([
+        'environment_id' => $environment->id,
+        'destination_id' => $destination->id,
+        'destination_type' => StandaloneDocker::class,
+        'source_id' => $systemGithubApp->id,
+        'source_type' => GithubApp::class,
+    ]);
+
+    // Delete the target user — should NOT throw or delete the system-wide GitHub App
+    $targetUser->delete();
+
+    // Assert user is deleted
+    expect(User::find($targetUser->id))->toBeNull();
+
+    // Assert the system-wide GitHub App still exists
+    expect(GithubApp::find($systemGithubApp->id))->not->toBeNull();
+});
+
+it('transfers instance-wide github app to root team when owning user is deleted', function () {
+    // Create a user whose team owns an instance-wide GitHub App
+    $targetUser = User::factory()->create();
+    $targetTeam = $targetUser->teams()->first();
+
+    $targetPrivateKey = PrivateKey::factory()->create(['team_id' => $targetTeam->id]);
+    $instanceWideApp = GithubApp::create([
+        'name' => 'Instance-Wide GitHub App',
+        'team_id' => $targetTeam->id,
+        'private_key_id' => $targetPrivateKey->id,
+        'api_url' => 'https://api.github.com',
+        'html_url' => 'https://github.com',
+        'is_public' => false,
+        'is_system_wide' => true,
+    ]);
+
+    // Create an application on the ROOT team that uses this instance-wide GitHub App
+    $rootPrivateKey = PrivateKey::factory()->create(['team_id' => $this->rootTeam->id]);
+    $rootServer = Server::factory()->create([
+        'team_id' => $this->rootTeam->id,
+        'private_key_id' => $rootPrivateKey->id,
+    ]);
+    $rootDestination = StandaloneDocker::factory()->create(['server_id' => $rootServer->id]);
+    $rootProject = Project::factory()->create(['team_id' => $this->rootTeam->id]);
+    $rootEnvironment = Environment::factory()->create(['project_id' => $rootProject->id]);
+
+    $otherTeamApp = Application::factory()->create([
+        'environment_id' => $rootEnvironment->id,
+        'destination_id' => $rootDestination->id,
+        'destination_type' => StandaloneDocker::class,
+        'source_id' => $instanceWideApp->id,
+        'source_type' => GithubApp::class,
+    ]);
+
+    // Delete the user — should succeed and transfer the instance-wide app to root team
+    $targetUser->delete();
+
+    // Assert user is deleted
+    expect(User::find($targetUser->id))->toBeNull();
+
+    // Assert the instance-wide GitHub App is preserved and transferred to root team
+    $instanceWideApp->refresh();
+    expect($instanceWideApp)->not->toBeNull();
+    expect($instanceWideApp->team_id)->toBe($this->rootTeam->id);
+
+    // Assert the other team's application still has its source intact
+    $otherTeamApp->refresh();
+    expect($otherTeamApp->source_id)->toBe($instanceWideApp->id);
+    expect($otherTeamApp->source_type)->toBe(GithubApp::class);
+});
+
+it('transfers instance-wide github app to root team when team is deleted directly', function () {
+    // Create a team that owns an instance-wide GitHub App
+    $targetUser = User::factory()->create();
+    $targetTeam = $targetUser->teams()->first();
+
+    $targetPrivateKey = PrivateKey::factory()->create(['team_id' => $targetTeam->id]);
+    $instanceWideApp = GithubApp::create([
+        'name' => 'Instance-Wide GitHub App',
+        'team_id' => $targetTeam->id,
+        'private_key_id' => $targetPrivateKey->id,
+        'api_url' => 'https://api.github.com',
+        'html_url' => 'https://github.com',
+        'is_public' => false,
+        'is_system_wide' => true,
+    ]);
+
+    // Create an application on the ROOT team that uses this instance-wide GitHub App
+    $rootPrivateKey = PrivateKey::factory()->create(['team_id' => $this->rootTeam->id]);
+    $rootServer = Server::factory()->create([
+        'team_id' => $this->rootTeam->id,
+        'private_key_id' => $rootPrivateKey->id,
+    ]);
+    $rootDestination = StandaloneDocker::factory()->create(['server_id' => $rootServer->id]);
+    $rootProject = Project::factory()->create(['team_id' => $this->rootTeam->id]);
+    $rootEnvironment = Environment::factory()->create(['project_id' => $rootProject->id]);
+
+    $otherTeamApp = Application::factory()->create([
+        'environment_id' => $rootEnvironment->id,
+        'destination_id' => $rootDestination->id,
+        'destination_type' => StandaloneDocker::class,
+        'source_id' => $instanceWideApp->id,
+        'source_type' => GithubApp::class,
+    ]);
+
+    // Delete the team directly — should transfer instance-wide app to root team
+    $targetTeam->delete();
+
+    // Assert the instance-wide GitHub App is preserved and transferred to root team
+    $instanceWideApp->refresh();
+    expect($instanceWideApp)->not->toBeNull();
+    expect($instanceWideApp->team_id)->toBe($this->rootTeam->id);
+
+    // Assert the other team's application still has its source intact
+    $otherTeamApp->refresh();
+    expect($otherTeamApp->source_id)->toBe($instanceWideApp->id);
+    expect($otherTeamApp->source_type)->toBe(GithubApp::class);
+});