diff --git a/app/Jobs/ApplicationDeploymentJob.php b/app/Jobs/ApplicationDeploymentJob.php
index c429a8ae20..9287e2030d 100644
--- a/app/Jobs/ApplicationDeploymentJob.php
+++ b/app/Jobs/ApplicationDeploymentJob.php
@@ -2609,6 +2609,7 @@ class ApplicationDeploymentJob implements ShouldBeEncrypted, ShouldQueue
             $nixpacks_php_fallback_path->value = '/index.php';
             $nixpacks_php_fallback_path->resourceable_id = $this->application->id;
             $nixpacks_php_fallback_path->resourceable_type = 'App\Models\Application';
+            $nixpacks_php_fallback_path->is_preview = $this->pull_request_id !== 0;
             $nixpacks_php_fallback_path->save();
         }
         if (! $nixpacks_php_root_dir) {
@@ -2617,6 +2618,7 @@ class ApplicationDeploymentJob implements ShouldBeEncrypted, ShouldQueue
             $nixpacks_php_root_dir->value = '/app/public';
             $nixpacks_php_root_dir->resourceable_id = $this->application->id;
             $nixpacks_php_root_dir->resourceable_type = 'App\Models\Application';
+            $nixpacks_php_root_dir->is_preview = $this->pull_request_id !== 0;
             $nixpacks_php_root_dir->save();
         }
 
diff --git a/app/Models/Application.php b/app/Models/Application.php
index 2b14b3c86b..fc9085752c 100644
--- a/app/Models/Application.php
+++ b/app/Models/Application.php
@@ -1168,7 +1168,7 @@ class Application extends BaseModel
     {
         return $this->morphMany(EnvironmentVariable::class, 'resourceable')
             ->where('is_preview', false)
-            ->withoutBuildpackControlVariables();
+            ->withoutBuildOnlyBuildpackControlVariables();
     }
 
     public function nixpacks_environment_variables()
@@ -1203,7 +1203,7 @@ class Application extends BaseModel
     {
         return $this->morphMany(EnvironmentVariable::class, 'resourceable')
             ->where('is_preview', true)
-            ->withoutBuildpackControlVariables();
+            ->withoutBuildOnlyBuildpackControlVariables();
     }
 
     public function nixpacks_environment_variables_preview()
diff --git a/app/Models/EnvironmentVariable.php b/app/Models/EnvironmentVariable.php
index acb4ca139f..81ac70023c 100644
--- a/app/Models/EnvironmentVariable.php
+++ b/app/Models/EnvironmentVariable.php
@@ -44,6 +44,17 @@ class EnvironmentVariable extends BaseModel
 
     public const BUILDPACK_CONTROL_VARIABLE_PREFIXES = ['NIXPACKS_', 'RAILPACK_'];
 
+    /**
+     * Buildpack control variables that the built image reads when the container starts,
+     * e.g. the Nixpacks PHP prestart script renders nginx.conf from NIXPACKS_PHP_ROOT_DIR.
+     */
+    public const RUNTIME_BUILDPACK_CONTROL_VARIABLES = [
+        'NIXPACKS_PHP_ROOT_DIR',
+        'NIXPACKS_PHP_FALLBACK_PATH',
+        'NIXPACKS_SPA_OUTPUT_DIR',
+        'RAILPACK_SKIP_MIGRATIONS',
+    ];
+
     protected $attributes = [
         'is_runtime' => true,
         'is_buildtime' => true,
@@ -163,6 +174,14 @@ class EnvironmentVariable extends BaseModel
         return $query;
     }
 
+    public function scopeWithoutBuildOnlyBuildpackControlVariables(Builder $query): Builder
+    {
+        return $query->where(function (Builder $query) {
+            $query->whereIn('key', self::RUNTIME_BUILDPACK_CONTROL_VARIABLES)
+                ->orWhere(fn (Builder $query) => $query->withoutBuildpackControlVariables());
+        });
+    }
+
     public static function isBuildpackControlKey(?string $key): bool
     {
         if (blank($key)) {
diff --git a/tests/Feature/ApplicationDeploymentControlVarFilteringTest.php b/tests/Feature/ApplicationDeploymentControlVarFilteringTest.php
index b3248f2d8d..f17a59e5df 100644
--- a/tests/Feature/ApplicationDeploymentControlVarFilteringTest.php
+++ b/tests/Feature/ApplicationDeploymentControlVarFilteringTest.php
@@ -943,6 +943,93 @@ it('filters buildpack control vars from preview runtime env fallback', function
     expect($runtimeEnvs->contains(fn (string $env) => str($env)->startsWith('RAILPACK_NODE_VERSION=')))->toBeFalse();
 });
 
+it('keeps buildpack variables read at container start in the runtime env', function (int $pullRequestId, bool $isPreview) {
+    [$application, $server] = makeDeploymentControlVarFixture(['build_pack' => 'nixpacks']);
+
+    foreach ([
+        'APP_NAME' => 'coolify',
+        'NIXPACKS_PHP_ROOT_DIR' => '/app/public',
+        'NIXPACKS_PHP_FALLBACK_PATH' => '/index.php',
+        'NIXPACKS_SPA_OUTPUT_DIR' => 'dist',
+        'RAILPACK_SKIP_MIGRATIONS' => 'true',
+        'NIXPACKS_NODE_VERSION' => '22',
+        'RAILPACK_NODE_VERSION' => '20',
+    ] as $key => $value) {
+        createApplicationEnvironmentVariable($application, [
+            'key' => $key,
+            'value' => $value,
+            'is_preview' => $isPreview,
+        ]);
+    }
+
+    [$job, $reflection] = makeControlVarFilteringJob($application, $server, [
+        'pull_request_id' => $pullRequestId,
+    ]);
+
+    /** @var Collection $runtimeEnvs */
+    $runtimeEnvs = invokeDeploymentJobMethod($job, $reflection, 'generate_runtime_environment_variables');
+
+    expect($runtimeEnvs)->toContain(
+        'APP_NAME='.escapeComposeEnvFileValue('coolify'),
+        'NIXPACKS_PHP_ROOT_DIR='.escapeComposeEnvFileValue('/app/public'),
+        'NIXPACKS_PHP_FALLBACK_PATH='.escapeComposeEnvFileValue('/index.php'),
+        'NIXPACKS_SPA_OUTPUT_DIR='.escapeComposeEnvFileValue('dist'),
+        'RAILPACK_SKIP_MIGRATIONS='.escapeComposeEnvFileValue('true'),
+    );
+    expect($runtimeEnvs->contains(fn (string $env) => str($env)->startsWith('NIXPACKS_NODE_VERSION=')))->toBeFalse();
+    expect($runtimeEnvs->contains(fn (string $env) => str($env)->startsWith('RAILPACK_NODE_VERSION=')))->toBeFalse();
+})->with([
+    'production' => [0, false],
+    'preview' => [42, true],
+]);
+
+it('keeps buildpack variables read at container start out of generic build args', function () {
+    [$application, $server] = makeDeploymentControlVarFixture();
+
+    createApplicationEnvironmentVariable($application, [
+        'key' => 'NIXPACKS_PHP_ROOT_DIR',
+        'value' => '/app/public',
+    ]);
+    createApplicationEnvironmentVariable($application, [
+        'key' => 'RAILPACK_SKIP_MIGRATIONS',
+        'value' => 'true',
+    ]);
+
+    [$job, $reflection] = makeControlVarFilteringJob($application, $server);
+
+    invokeDeploymentJobMethod($job, $reflection, 'generate_env_variables');
+
+    /** @var Collection $envArgs */
+    $envArgs = readDeploymentJobProperty($job, $reflection, 'env_args');
+
+    expect($envArgs->has('NIXPACKS_PHP_ROOT_DIR'))->toBeFalse();
+    expect($envArgs->has('RAILPACK_SKIP_MIGRATIONS'))->toBeFalse();
+});
+
+it('creates missing Laravel defaults as preview variables for preview deployments', function () {
+    [$application, $server] = makeDeploymentControlVarFixture(['build_pack' => 'nixpacks']);
+
+    $keys = ['NIXPACKS_PHP_ROOT_DIR', 'NIXPACKS_PHP_FALLBACK_PATH'];
+    foreach (array_combine($keys, ['/app/web', '/app.php']) as $key => $value) {
+        createApplicationEnvironmentVariable($application, ['key' => $key, 'value' => $value]);
+    }
+    $application->environment_variables_preview()->whereIn('key', $keys)->delete();
+
+    [$job, $reflection] = makeControlVarFilteringJob($application, $server, ['pull_request_id' => 42]);
+
+    [$fallbackPath, $rootDir] = invokeDeploymentJobMethod($job, $reflection, 'laravel_finetunes');
+
+    expect($fallbackPath->is_preview)->toBeTrue()
+        ->and($fallbackPath->value)->toBe('/index.php')
+        ->and($rootDir->is_preview)->toBeTrue()
+        ->and($rootDir->value)->toBe('/app/public')
+        ->and($application->environment_variables()->whereIn('key', $keys)->pluck('value', 'key')->all())->toBe([
+            'NIXPACKS_PHP_ROOT_DIR' => '/app/web',
+            'NIXPACKS_PHP_FALLBACK_PATH' => '/app.php',
+        ])
+        ->and($application->environment_variables_preview()->whereIn('key', $keys)->count())->toBe(2);
+});
+
 it('filters buildpack control vars from dockerfile arg injection', function () {
     [$application, $server] = makeDeploymentControlVarFixture();