diff --git a/app/Livewire/Project/Shared/EnvironmentVariable/All.php b/app/Livewire/Project/Shared/EnvironmentVariable/All.php
index ea8394c1b1..47080cd86b 100644
--- a/app/Livewire/Project/Shared/EnvironmentVariable/All.php
+++ b/app/Livewire/Project/Shared/EnvironmentVariable/All.php
@@ -818,19 +818,21 @@ class All extends Component
     {
         $isMember = auth()->user()?->isMember();
 
-        return $variables->map(function ($item) use ($isMember) {
-            if ($isMember) {
-                return "$item->key=(Hidden, only admins can view)";
-            }
-            if ($item->is_shown_once) {
-                return "$item->key=(Locked Secret, delete and add again to change)";
-            }
-            if ($item->is_multiline) {
-                return "$item->key=(Multiline environment variable, edit in normal view)";
-            }
+        return $variables
+            ->reject(fn ($item): bool => $this->isProtectedEnvironmentVariable($item->key))
+            ->map(function ($item) use ($isMember) {
+                if ($isMember) {
+                    return "$item->key=(Hidden, only admins can view)";
+                }
+                if ($item->is_shown_once) {
+                    return "$item->key=(Locked Secret, delete and add again to change)";
+                }
+                if ($item->is_multiline) {
+                    return "$item->key=(Multiline environment variable, edit in normal view)";
+                }
 
-            return "$item->key=$item->value";
-        })->join("\n");
+                return "$item->key=$item->value";
+            })->join("\n");
     }
 
     public function switch()
@@ -908,8 +910,7 @@ class All extends Component
         $deletedCount = $this->deleteRemovedVariables(false, $variables);
         if ($deletedCount > 0) {
             $changesMade = true;
-        } elseif ($deletedCount === 0 && $this->resource->environment_variables()->whereNotIn('key', array_keys($variables))->exists()) {
-            // If we tried to delete but couldn't (due to Docker Compose), mark as error
+        } elseif ($deletedCount < 0) {
             $errorOccurred = true;
         }
 
@@ -926,8 +927,7 @@ class All extends Component
             $deletedPreviewCount = $this->deleteRemovedVariables(true, $previewVariables);
             if ($deletedPreviewCount > 0) {
                 $changesMade = true;
-            } elseif ($deletedPreviewCount === 0 && $this->resource->environment_variables_preview()->whereNotIn('key', array_keys($previewVariables))->exists()) {
-                // If we tried to delete but couldn't (due to Docker Compose), mark as error
+            } elseif ($deletedPreviewCount < 0) {
                 $errorOccurred = true;
             }
 
@@ -988,6 +988,12 @@ class All extends Component
         // Get all environment variables that will be deleted
         $variablesToDelete = $this->resource->$method()->whereNotIn('key', array_keys($variables))->get();
 
+        // Generated Compose variables are managed by Coolify and must survive a bulk
+        // replacement even when they are omitted from the pasted environment file.
+        $variablesToDelete = $variablesToDelete->reject(
+            fn (EnvironmentVariable $environmentVariable): bool => $this->isProtectedEnvironmentVariable($environmentVariable->key)
+        );
+
         // If there are no variables to delete, return 0
         if ($variablesToDelete->isEmpty()) {
             return 0;
@@ -1001,13 +1007,13 @@ class All extends Component
                 if ($isUsed) {
                     $this->dispatch('error', "Cannot delete environment variable '{$envVar->key}' <br><br>Please remove it from the Docker Compose file first.");
 
-                    return 0;
+                    return -1;
                 }
             }
         }
 
         // If we get here, no variables are used in Docker Compose, so we can delete them
-        $this->resource->$method()->whereNotIn('key', array_keys($variables))->delete();
+        $this->resource->$method()->whereKey($variablesToDelete->modelKeys())->delete();
 
         return $variablesToDelete->count();
     }
diff --git a/tests/Feature/EnvironmentVariableAsyncLoadTest.php b/tests/Feature/EnvironmentVariableAsyncLoadTest.php
index 2cbc5537a1..4d83862b6e 100644
--- a/tests/Feature/EnvironmentVariableAsyncLoadTest.php
+++ b/tests/Feature/EnvironmentVariableAsyncLoadTest.php
@@ -121,3 +121,69 @@ it('is idempotent when loadEnvironmentVariables is called twice', function () {
     expect($component->instance()->environmentVariables->pluck('key')->all())
         ->toContain('API_KEY');
 });
+
+it('preserves generated compose variables during bulk replacement', function () {
+    $application = Application::factory()->create([
+        'environment_id' => $this->environment->id,
+        'build_pack' => 'dockercompose',
+        'docker_compose' => <<<'YAML'
+services:
+  api:
+    image: nginx:alpine
+    environment:
+      SERVICE_URL_API: /api
+YAML,
+    ]);
+
+    foreach ([
+        'SERVICE_URL_API' => 'https://api.example.com/api',
+        'SERVICE_FQDN_API' => 'api.example.com/api',
+        'OLD_VARIABLE' => 'remove-me',
+    ] as $key => $value) {
+        EnvironmentVariable::create([
+            'key' => $key,
+            'value' => $value,
+            'resourceable_type' => Application::class,
+            'resourceable_id' => $application->id,
+        ]);
+    }
+
+    Livewire::test(All::class, ['resource' => $application])
+        ->set('variables', 'NEW_VARIABLE=keep-me')
+        ->call('submit')
+        ->assertDispatched('success')
+        ->assertNotDispatched('error');
+
+    expect($application->environment_variables()->pluck('value', 'key')->all())
+        ->toBe([
+            'SERVICE_URL_API' => 'https://api.example.com/api',
+            'SERVICE_FQDN_API' => 'api.example.com/api',
+            'NEW_VARIABLE' => 'keep-me',
+        ]);
+});
+
+it('hides generated compose variables from developer view', function () {
+    $application = Application::factory()->create([
+        'environment_id' => $this->environment->id,
+        'build_pack' => 'dockercompose',
+    ]);
+
+    foreach ([
+        'SERVICE_URL_API' => 'https://api.example.com',
+        'SERVICE_FQDN_API' => 'api.example.com',
+        'API_URL' => '$SERVICE_URL_API',
+    ] as $key => $value) {
+        EnvironmentVariable::create([
+            'key' => $key,
+            'value' => $value,
+            'resourceable_type' => Application::class,
+            'resourceable_id' => $application->id,
+        ]);
+    }
+
+    $component = Livewire::test(All::class, ['resource' => $application])
+        ->call('switch');
+
+    expect($component->get('variables'))
+        ->toBe('API_URL=$SERVICE_URL_API');
+});