diff --git a/src/Builder/Concerns/PrunesVendorDirectory.php b/src/Builder/Concerns/PrunesVendorDirectory.php
index 7551aaf1..4d60b380 100644
--- a/src/Builder/Concerns/PrunesVendorDirectory.php
+++ b/src/Builder/Concerns/PrunesVendorDirectory.php
@@ -24,10 +24,14 @@ public function pruneVendorDirectory()
             $this->buildPath('app/vendor/nativephp/php-bin'),
         ]);
 
-        // Remove custom php binary package directory
-        $binaryPackageDirectory = $this->binaryPackageDirectory();
-        if (! empty($binaryPackageDirectory) && $filesystem->exists($this->buildPath("app/{$binaryPackageDirectory}"))) {
-            $filesystem->remove($this->buildPath("app/{$binaryPackageDirectory}"));
-        }
+        // Remove the bundled PHP binaries for a custom binary path.
+        // They get duplicated into the app's build resources, so
+        // the copies left in the source tree are dead weight.
+        //
+        // We remove only the archives we manage, never the
+        // parent directory, so the user's files are kept,
+        // and a root path never wipes the app (#115).
+        $binaryDirectory = $this->buildPath('app/'.$this->binaryPackageDirectory().'bin');
+        $filesystem->remove(glob("{$binaryDirectory}/*/*/php-*.zip"));
     }
 }
diff --git a/src/Client/Client.php b/src/Client/Client.php
index d6dd7749..cbafee66 100644
--- a/src/Client/Client.php
+++ b/src/Client/Client.php
@@ -16,7 +16,7 @@ public function __construct()
             ->baseUrl(config('nativephp-internal.api_url', ''))
             ->timeout(60 * 60)
             ->withHeaders([
-                'X-NativePHP-Secret' => config('nativephp-internal.secret'),
+                'X-NativePHP-Secret' => (string) config('nativephp-internal.secret'),
             ])
             ->asJson();
     }
diff --git a/tests/Build/PruneVendorDirectoryTest.php b/tests/Build/PruneVendorDirectoryTest.php
new file mode 100644
index 00000000..c85d56de
--- /dev/null
+++ b/tests/Build/PruneVendorDirectoryTest.php
@@ -0,0 +1,101 @@
+<?php
+
+use Illuminate\Support\Facades\Process;
+use Native\Desktop\Builder\Concerns\LocatesPhpBinary;
+use Native\Desktop\Builder\Concerns\PrunesVendorDirectory;
+use Symfony\Component\Filesystem\Filesystem;
+
+/*
+|--------------------------------------------------------------------------
+| Setup
+|--------------------------------------------------------------------------
+*/
+$buildPath = testsDir('_test_build_path');
+
+beforeEach(function () use ($buildPath) {
+    Process::fake();
+
+    $filesystem = new Filesystem;
+    $filesystem->remove($buildPath);
+});
+
+afterEach(function () use ($buildPath) {
+    putenv('NATIVEPHP_PHP_BINARY_PATH');
+
+    $filesystem = new Filesystem;
+    $filesystem->remove($buildPath);
+});
+
+/*
+|--------------------------------------------------------------------------
+| Mock Build command with anonymous class
+|--------------------------------------------------------------------------
+*/
+$command = new class($buildPath)
+{
+    use LocatesPhpBinary;
+    use PrunesVendorDirectory;
+
+    public function __construct(
+        public $buildPath
+    ) {}
+
+    public function sourcePath(string $path = ''): string
+    {
+        return app()->joinPaths($this->buildPath, $path);
+    }
+
+    public function buildPath(string $path = ''): string
+    {
+        return app()->joinPaths($this->buildPath, $path);
+    }
+};
+
+/*
+|--------------------------------------------------------------------------
+| Tests
+|--------------------------------------------------------------------------
+*/
+it('prunes the bundled php binary archives from a custom binary directory', function () use ($buildPath, $command) {
+    putenv('NATIVEPHP_PHP_BINARY_PATH=php-bin/');
+
+    createFiles([
+        "$buildPath/app/index.php",
+        "$buildPath/app/php-bin/bin/win/x64/php-8.4.zip",
+        "$buildPath/app/php-bin/bin/mac/arm64/php-8.4.zip",
+    ]);
+
+    $command->pruneVendorDirectory();
+
+    // The redundant archives are stripped...
+    expect("$buildPath/app/php-bin/bin/win/x64/php-8.4.zip")->not->toBeFile();
+    expect("$buildPath/app/php-bin/bin/mac/arm64/php-8.4.zip")->not->toBeFile();
+
+    // ...while the rest of the app is left intact.
+    expect("$buildPath/app/index.php")->toBeFile();
+});
+
+it('does not delete the app when the binary path is the project root', function () use ($buildPath, $command) {
+    // Regression test for #115: a binary path that normalises to the app root
+    // (e.g. binaries kept directly in the project's bin/ directory) must not
+    // take the whole app down with the prune.
+    putenv('NATIVEPHP_PHP_BINARY_PATH=./');
+
+    createFiles([
+        "$buildPath/app/index.php",
+        "$buildPath/app/bin/win/x64/php-8.4.zip",
+        "$buildPath/app/bin/mac/arm64/php-8.4.zip",
+        // Unrelated tooling a user happens to keep in bin/ must survive.
+        "$buildPath/app/bin/deploy.sh",
+    ]);
+
+    $command->pruneVendorDirectory();
+
+    // The app and any non-NativePHP files in bin/ are preserved...
+    expect("$buildPath/app/index.php")->toBeFile();
+    expect("$buildPath/app/bin/deploy.sh")->toBeFile();
+
+    // ...but the bundled php archives are still pruned.
+    expect("$buildPath/app/bin/win/x64/php-8.4.zip")->not->toBeFile();
+    expect("$buildPath/app/bin/mac/arm64/php-8.4.zip")->not->toBeFile();
+});