diff --git a/pkg/dartdev/lib/src/commands/compile.dart b/pkg/dartdev/lib/src/commands/compile.dart
index 600c1c257d1..bf5b15e992d 100644
--- a/pkg/dartdev/lib/src/commands/compile.dart
+++ b/pkg/dartdev/lib/src/commands/compile.dart
@@ -709,17 +709,26 @@ Remove debugging information from the output and save it separately to the speci
           verbose: verbose,
           target: target,
         );
-        if (!nativeAssetsExperimentEnabled) {
-          if (await builder.warnOnNativeAssets()) {
+
+        final isBinScript = path.isWithin(
+          path.canonicalize(path.join(Directory.current.path, 'bin')),
+          path.canonicalize(sourcePath),
+        );
+        if (isBinScript) {
+          if (!nativeAssetsExperimentEnabled) {
+            if (await builder.warnOnNativeAssets()) {
+              return 255;
+            }
+          } else if (await builder.hasHooks()) {
+            final packages = (await builder.packagesWithBuildHooks()).join(
+              ', ',
+            );
+            stderr.writeln(
+              "'dart compile' does not support build hooks, use 'dart build' instead.\n"
+              'Packages with build hooks: $packages.',
+            );
             return 255;
           }
-        } else if (await builder.hasHooks()) {
-          final packages = (await builder.packagesWithBuildHooks()).join(', ');
-          stderr.writeln(
-            "'dart compile' does not support build hooks, use 'dart build' instead.\n"
-            'Packages with build hooks: $packages.',
-          );
-          return 255;
         }
       }
     }
diff --git a/pkg/dartdev/test/native_assets/compile_test.dart b/pkg/dartdev/test/native_assets/compile_test.dart
index b46c40649d9..31170087f88 100644
--- a/pkg/dartdev/test/native_assets/compile_test.dart
+++ b/pkg/dartdev/test/native_assets/compile_test.dart
@@ -49,6 +49,58 @@ void main() async {
     });
   });
 
+  test('dart compile only bails in bin/', timeout: longTimeout, () async {
+    await nativeAssetsTest('dart_app', (dartAppUri) async {
+      await runDart(
+        arguments: ['pub', 'get'],
+        workingDirectory: dartAppUri,
+        logger: logger,
+      );
+
+      // 1. Compiling in bin/ should fail.
+      final resultBin = await runDart(
+        arguments: [
+          'compile',
+          'exe',
+          'bin/dart_app.dart',
+        ],
+        workingDirectory: dartAppUri,
+        logger: logger,
+        expectExitCodeZero: false,
+      );
+      expect(resultBin.exitCode, 255);
+      expect(
+        resultBin.stderr,
+        contains(
+          "'dart compile' does not support build hooks, use 'dart build' instead.",
+        ),
+      );
+
+      // 2. Compiling outside bin/ should succeed (even if it might fail at runtime).
+      final otherFile = File.fromUri(dartAppUri.resolve('tool/other.dart'));
+      await otherFile.parent.create(recursive: true);
+      await otherFile.writeAsString('void main() { print("hello"); }');
+
+      final resultOther = await runDart(
+        arguments: [
+          '-v',
+          'compile',
+          'exe',
+          'tool/other.dart',
+        ],
+        workingDirectory: dartAppUri,
+        logger: logger,
+      );
+      expect(resultOther.exitCode, 0);
+      final exePath = dartAppUri.resolve('tool/other.exe').toFilePath();
+      final resultRun = await runProcess(
+        executable: Uri.file(exePath),
+        logger: logger,
+      );
+      expect(resultRun.stdout, contains('hello'));
+    });
+  });
+
   test('Recorded usages in dart2js', timeout: longTimeout, () async {
     await recordUseTest('drop_data_asset', (dartAppUri) async {
       await runDart(