diff --git a/pkgs/native_assets_builder/lib/src/build_runner/build_runner.dart b/pkgs/native_assets_builder/lib/src/build_runner/build_runner.dart
index 4e5e571d8..07c4c40b7 100644
--- a/pkgs/native_assets_builder/lib/src/build_runner/build_runner.dart
+++ b/pkgs/native_assets_builder/lib/src/build_runner/build_runner.dart
@@ -326,8 +326,8 @@ class NativeAssetsBuildRunner {
     return await runUnderDirectoriesLock(
       _fileSystem,
       [
-        _fileSystem.directory(config.outputDirectoryShared).parent,
-        _fileSystem.directory(config.outputDirectory).parent,
+        _fileSystem.directory(config.outputDirectoryShared).parent.uri,
+        _fileSystem.directory(config.outputDirectory).parent.uri,
       ],
       timeout: singleHookTimeout,
       logger: logger,
@@ -346,14 +346,12 @@ class NativeAssetsBuildRunner {
 
         final buildOutputFile =
             _fileSystem.file(config.outputDirectory.resolve(hook.outputName));
-        final dependenciesHashFile = _fileSystem.file(
-          config.outputDirectory
-              .resolve('../dependencies.dependencies_hash_file.json'),
-        );
+        final dependenciesHashFile = config.outputDirectory
+            .resolve('../dependencies.dependencies_hash_file.json');
         final dependenciesHashes =
-            DependenciesHashFile(_fileSystem, file: dependenciesHashFile);
+            DependenciesHashFile(_fileSystem, fileUri: dependenciesHashFile);
         final lastModifiedCutoffTime = DateTime.now();
-        if (buildOutputFile.existsSync() && dependenciesHashFile.existsSync()) {
+        if (buildOutputFile.existsSync() && await dependenciesHashes.exists()) {
           late final HookOutput output;
           try {
             output = _readHookOutputFromUri(hook, buildOutputFile);
@@ -398,8 +396,8 @@ ${e.message}
           environment,
         );
         if (result == null) {
-          if (await dependenciesHashFile.exists()) {
-            await dependenciesHashFile.delete();
+          if (await dependenciesHashes.exists()) {
+            await dependenciesHashes.delete();
           }
           return null;
         } else {
@@ -468,6 +466,7 @@ ${e.message}
       if (resources != null) resources.toFilePath(),
     ];
     final result = await runProcess(
+      filesystem: _fileSystem,
       workingDirectory: workingDirectory,
       executable: dartExecutable,
       arguments: arguments,
@@ -572,14 +571,13 @@ ${e.message}
     final depFile = _fileSystem.file(
       outputDirectory.resolve('../hook.dill.d'),
     );
-    final dependenciesHashFile = _fileSystem.file(
-      outputDirectory.resolve('../hook.dependencies_hash_file.json'),
-    );
+    final dependenciesHashFile =
+        outputDirectory.resolve('../hook.dependencies_hash_file.json');
     final dependenciesHashes =
-        DependenciesHashFile(_fileSystem, file: dependenciesHashFile);
+        DependenciesHashFile(_fileSystem, fileUri: dependenciesHashFile);
     final lastModifiedCutoffTime = DateTime.now();
     var mustCompile = false;
-    if (!await dependenciesHashFile.exists()) {
+    if (!await dependenciesHashes.exists()) {
       mustCompile = true;
     } else {
       final outdatedDependency = await dependenciesHashes
@@ -642,6 +640,7 @@ ${e.message}
       scriptUri.toFilePath(),
     ];
     final compileResult = await runProcess(
+      filesystem: _fileSystem,
       workingDirectory: workingDirectory,
       executable: dartExecutable,
       arguments: compileArguments,
diff --git a/pkgs/native_assets_builder/lib/src/dependencies_hash_file/dependencies_hash_file.dart b/pkgs/native_assets_builder/lib/src/dependencies_hash_file/dependencies_hash_file.dart
index 681e14586..2c2f9c806 100644
--- a/pkgs/native_assets_builder/lib/src/dependencies_hash_file/dependencies_hash_file.dart
+++ b/pkgs/native_assets_builder/lib/src/dependencies_hash_file/dependencies_hash_file.dart
@@ -15,16 +15,20 @@ import '../utils/uri.dart';
 class DependenciesHashFile {
   DependenciesHashFile(
     this._fileSystem, {
-    required this.file,
+    required this.fileUri,
   });
 
   final FileSystem _fileSystem;
-  final File file;
+  final Uri fileUri;
   FileSystemHashes _hashes = FileSystemHashes();
 
   List<Uri> get fileSystemEntities => _hashes.files.map((e) => e.path).toList();
 
+  Future<bool> exists() async => await _fileSystem.file(fileUri).exists();
+  Future<void> delete() async => await _fileSystem.file(fileUri).delete();
+
   Future<void> _readFile() async {
+    final file = _fileSystem.file(fileUri);
     if (!await file.exists()) {
       _hashes = FileSystemHashes();
       return;
@@ -75,7 +79,8 @@ class DependenciesHashFile {
     return modifiedAfterTimeStamp;
   }
 
-  Future<void> _persist() => file.writeAsString(json.encode(_hashes.toJson()));
+  Future<void> _persist() =>
+      _fileSystem.file(fileUri).writeAsString(json.encode(_hashes.toJson()));
 
   /// Reads the file with hashes and reports if there is an outdated file,
   /// directory or environment variable.
diff --git a/pkgs/native_assets_builder/lib/src/locking/locking.dart b/pkgs/native_assets_builder/lib/src/locking/locking.dart
index f2351233f..7a1c26f73 100644
--- a/pkgs/native_assets_builder/lib/src/locking/locking.dart
+++ b/pkgs/native_assets_builder/lib/src/locking/locking.dart
@@ -10,7 +10,7 @@ import 'package:logging/logging.dart';
 
 Future<T> runUnderDirectoriesLock<T>(
   FileSystem fileSystem,
-  List<Directory> directories,
+  List<Uri> directories,
   Future<T> Function() callback, {
   Duration? timeout,
   Logger? logger,
@@ -46,13 +46,13 @@ Future<T> runUnderDirectoriesLock<T>(
 /// also streams error messages.
 Future<T> runUnderDirectoryLock<T>(
   FileSystem fileSystem,
-  Directory directory,
+  Uri directory,
   Future<T> Function() callback, {
   Duration? timeout,
   Logger? logger,
 }) async {
   const lockFileName = '.lock';
-  final lockFile = _fileInDir(fileSystem, directory, lockFileName);
+  final lockFile = _fileInDir(fileSystem.directory(directory), lockFileName);
   return _runUnderFileLock(
     lockFile,
     callback,
@@ -61,11 +61,11 @@ Future<T> runUnderDirectoryLock<T>(
   );
 }
 
-File _fileInDir(FileSystem fileSystem, Directory path, String filename) {
+File _fileInDir(Directory path, String filename) {
   final dirPath = path.path;
   var separator = Platform.pathSeparator;
   if (dirPath.endsWith(separator)) separator = '';
-  return fileSystem.file('$dirPath$separator$filename');
+  return path.fileSystem.file('$dirPath$separator$filename');
 }
 
 /// Run [callback] with this Dart process having exclusive access to [file].
diff --git a/pkgs/native_assets_builder/lib/src/package_layout/package_layout.dart b/pkgs/native_assets_builder/lib/src/package_layout/package_layout.dart
index 8e8c19871..1e24aa3b2 100644
--- a/pkgs/native_assets_builder/lib/src/package_layout/package_layout.dart
+++ b/pkgs/native_assets_builder/lib/src/package_layout/package_layout.dart
@@ -42,11 +42,17 @@ class PackageLayout {
     packageConfigUri = packageConfigUri.normalizePath();
     final rootPackageRoot = packageConfigUri.resolve('../');
     return PackageLayout._(
-        fileSystem, rootPackageRoot, packageConfig, packageConfigUri);
+      fileSystem,
+      rootPackageRoot,
+      packageConfig,
+      packageConfigUri,
+    );
   }
 
   static Future<PackageLayout> fromRootPackageRoot(
-      FileSystem fileSystem, Uri rootPackageRoot) async {
+    FileSystem fileSystem,
+    Uri rootPackageRoot,
+  ) async {
     rootPackageRoot = rootPackageRoot.normalizePath();
     final packageConfigUri =
         rootPackageRoot.resolve('.dart_tool/package_config.json');
diff --git a/pkgs/native_assets_builder/lib/src/utils/run_process.dart b/pkgs/native_assets_builder/lib/src/utils/run_process.dart
index efb712012..2da342848 100644
--- a/pkgs/native_assets_builder/lib/src/utils/run_process.dart
+++ b/pkgs/native_assets_builder/lib/src/utils/run_process.dart
@@ -4,8 +4,9 @@
 
 import 'dart:async';
 import 'dart:convert';
-import 'dart:io';
+import 'dart:io' show Platform, Process, ProcessException, ProcessResult;
 
+import 'package:file/file.dart';
 import 'package:logging/logging.dart';
 
 /// Runs a [Process].
@@ -15,6 +16,7 @@ import 'package:logging/logging.dart';
 /// If [captureOutput], captures stdout and stderr.
 // TODO(dacoharkes): Share between package:native_toolchain_c and here.
 Future<RunProcessResult> runProcess({
+  required FileSystem filesystem,
   required Uri executable,
   List<String> arguments = const [],
   Uri? workingDirectory,
@@ -25,8 +27,8 @@ Future<RunProcessResult> runProcess({
   int expectedExitCode = 0,
   bool throwOnUnexpectedExitCode = false,
 }) async {
-  final printWorkingDir =
-      workingDirectory != null && workingDirectory != Directory.current.uri;
+  final printWorkingDir = workingDirectory != null &&
+      workingDirectory != filesystem.currentDirectory.uri;
   final commandString = [
     if (printWorkingDir) '(cd ${workingDirectory.toFilePath()};',
     ...?environment?.entries.map((entry) => '${entry.key}=${entry.value}'),
diff --git a/pkgs/native_assets_builder/test/dependencies_hash_file/dependencies_hash_file_test.dart b/pkgs/native_assets_builder/test/dependencies_hash_file/dependencies_hash_file_test.dart
index dcd1b7e6b..b97dc1d91 100644
--- a/pkgs/native_assets_builder/test/dependencies_hash_file/dependencies_hash_file_test.dart
+++ b/pkgs/native_assets_builder/test/dependencies_hash_file/dependencies_hash_file_test.dart
@@ -37,8 +37,8 @@ void main() async {
       final tempSubDir = fileSystem.directory(tempUri.resolve('subdir/'));
       final subFile = fileSystem.file(tempSubDir.uri.resolve('bar.txt'));
 
-      final hashesFile = fileSystem.file(tempUri.resolve('hashes.json'));
-      final hashes = DependenciesHashFile(fileSystem, file: hashesFile);
+      final hashesFileUri = tempUri.resolve('hashes.json');
+      final hashes = DependenciesHashFile(fileSystem, fileUri: hashesFileUri);
 
       Future<void> reset() async {
         await tempFile.create(recursive: true);
diff --git a/pkgs/native_assets_builder/test/helpers.dart b/pkgs/native_assets_builder/test/helpers.dart
index 0242bcd06..c64a7f79e 100644
--- a/pkgs/native_assets_builder/test/helpers.dart
+++ b/pkgs/native_assets_builder/test/helpers.dart
@@ -5,6 +5,7 @@
 import 'dart:async';
 import 'dart:io';
 
+import 'package:file/local.dart' show LocalFileSystem;
 import 'package:logging/logging.dart';
 import 'package:native_assets_builder/src/utils/run_process.dart'
     as run_process;
@@ -75,6 +76,7 @@ Future<run_process.RunProcessResult> runProcess({
   bool throwOnUnexpectedExitCode = false,
 }) =>
     run_process.runProcess(
+      filesystem: const LocalFileSystem(),
       executable: executable,
       arguments: arguments,
       workingDirectory: workingDirectory,
diff --git a/pkgs/native_assets_builder/test/locking/locking_test_helper.dart b/pkgs/native_assets_builder/test/locking/locking_test_helper.dart
index 9332b9383..c807900ca 100644
--- a/pkgs/native_assets_builder/test/locking/locking_test_helper.dart
+++ b/pkgs/native_assets_builder/test/locking/locking_test_helper.dart
@@ -16,7 +16,7 @@ void main(List<String> args) async {
   print('locking directory');
   await runUnderDirectoryLock<void>(
     fileSystem,
-    directory,
+    directory.uri,
     timeout: timeout,
     () async {
       print('directory locked');