diff --git a/Makefile b/Makefile
index 1a4ec78..3276797 100644
--- a/Makefile
+++ b/Makefile
@@ -228,6 +228,19 @@ benchmark-local:
 	@echo "Running benchmarks locally with full workflow..."
 	./scripts/benchmarks/run-benchmarks-local.sh
 
+# Run benchmarks with native libraries (requires native_libs build tag)
+benchmark-native:
+	@echo "Running benchmarks with native libraries..."
+	go test -bench=. -benchmem -tags native_libs ./tests/benchmarks/...
+
+# Compare Go vs Native implementation performance
+benchmark-compare:
+	@echo "=== Go Implementation ==="
+	@go test -bench=. -benchmem ./tests/benchmarks/... 2>&1 | grep -E '(Benchmark|ns/op|allocs/op)' || true
+	@echo ""
+	@echo "=== Native Implementation ==="
+	@go test -bench=. -benchmem -tags native_libs ./tests/benchmarks/... 2>&1 | grep -E '(Benchmark|ns/op|allocs/op)' || echo "Native not available (build with: make native-build)"
+
 # Manage benchmark artifacts
 artifacts:
 	@echo "Managing benchmark artifacts..."
diff --git a/tests/benchmarks/dataset_hash_bench_native_test.go b/tests/benchmarks/dataset_hash_bench_native_test.go
new file mode 100644
index 0000000..c88a25a
--- /dev/null
+++ b/tests/benchmarks/dataset_hash_bench_native_test.go
@@ -0,0 +1,94 @@
+//go:build native_libs
+// +build native_libs
+
+package benchmarks
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/jfraeys/fetch_ml/internal/worker"
+)
+
+// BenchmarkDirOverallSHA256Hex_Native profiles the directory hashing with native implementation.
+// This benchmark only runs when built with -tags native_libs.
+func BenchmarkDirOverallSHA256Hex_Native(b *testing.B) {
+	// Create a temp directory structure resembling a dataset
+	tmpDir := b.TempDir()
+
+	// Create nested structure with files of varying sizes
+	sizes := []int{1024, 10240, 102400, 1024 * 1024} // 1KB to 1MB
+	for i, size := range sizes {
+		subdir := filepath.Join(tmpDir, "subdir", string(rune('a'+i)))
+		if err := os.MkdirAll(subdir, 0750); err != nil {
+			b.Fatal(err)
+		}
+		data := make([]byte, size)
+		for j := range data {
+			data[j] = byte(i + j%256)
+		}
+		if err := os.WriteFile(filepath.Join(subdir, "data.bin"), data, 0640); err != nil {
+			b.Fatal(err)
+		}
+	}
+
+	// Add some small metadata files
+	metaDir := filepath.Join(tmpDir, "meta")
+	if err := os.MkdirAll(metaDir, 0750); err != nil {
+		b.Fatal(err)
+	}
+	for i := 0; i < 10; i++ {
+		if err := os.WriteFile(
+			filepath.Join(metaDir, "file"+string(rune('0'+i))+".json"),
+			[]byte(`{"key": "value"}`),
+			0640,
+		); err != nil {
+			b.Fatal(err)
+		}
+	}
+
+	b.ResetTimer()
+	b.ReportAllocs()
+
+	for i := 0; i < b.N; i++ {
+		_, err := worker.DirOverallSHA256Hex(tmpDir)
+		if err != nil {
+			b.Fatal(err)
+		}
+	}
+}
+
+// BenchmarkDirOverallSHA256HexLarge_Native profiles with larger dataset simulation using native
+func BenchmarkDirOverallSHA256HexLarge_Native(b *testing.B) {
+	tmpDir := b.TempDir()
+
+	// Create 50 files of 100KB each = ~5MB total
+	for i := 0; i < 50; i++ {
+		subdir := filepath.Join(tmpDir, "data", string(rune('a'+i%26)))
+		if err := os.MkdirAll(subdir, 0750); err != nil {
+			b.Fatal(err)
+		}
+		data := make([]byte, 100*1024)
+		for j := range data {
+			data[j] = byte(i + j%256)
+		}
+		if err := os.WriteFile(
+			filepath.Join(subdir, "chunk"+string(rune('0'+i/26))+".bin"),
+			data,
+			0640,
+		); err != nil {
+			b.Fatal(err)
+		}
+	}
+
+	b.ResetTimer()
+	b.ReportAllocs()
+
+	for i := 0; i < b.N; i++ {
+		_, err := worker.DirOverallSHA256Hex(tmpDir)
+		if err != nil {
+			b.Fatal(err)
+		}
+	}
+}
diff --git a/tests/benchmarks/dataset_hash_bench_test.go b/tests/benchmarks/dataset_hash_bench_test.go
index 0b2e4da..f42dffd 100644
--- a/tests/benchmarks/dataset_hash_bench_test.go
+++ b/tests/benchmarks/dataset_hash_bench_test.go
@@ -1,3 +1,6 @@
+//go:build !native_libs
+// +build !native_libs
+
 package benchmarks
 
 import (
diff --git a/tests/benchmarks/go_native_leak_test.go b/tests/benchmarks/go_native_leak_test.go
index dc41932..81d15b2 100644
--- a/tests/benchmarks/go_native_leak_test.go
+++ b/tests/benchmarks/go_native_leak_test.go
@@ -10,7 +10,7 @@ import (
 // TestGoNativeLeakStress runs 1000 iterations through Go->C++ integration
 func TestGoNativeLeakStress(t *testing.T) {
 	tmpDir := t.TempDir()
-	
+
 	// Create multiple test files
 	for i := 0; i < 10; i++ {
 		content := make([]byte, 1024*1024) // 1MB each
@@ -31,33 +31,37 @@ func TestGoNativeLeakStress(t *testing.T) {
 		if len(hash) != 64 {
 			t.Fatalf("Hash %d: expected 64 chars, got %d", i, len(hash))
 		}
-		
+
 		if i%100 == 0 {
 			t.Logf("Completed %d iterations", i)
 		}
 	}
-	
+
 	t.Logf("Completed 1000 iterations through Go->C++ integration")
 }
 
 // TestGoNativeArtifactScanLeak tests artifact scanner through Go
 func TestGoNativeArtifactScanLeak(t *testing.T) {
+	if !worker.HasSIMDSHA256() {
+		t.Skip("Native libraries not available (build with -tags native_libs)")
+	}
+
 	tmpDir := t.TempDir()
-	
+
 	// Create test files
 	for i := 0; i < 50; i++ {
 		if err := os.WriteFile(tmpDir+"/file_"+string(rune('a'+i%26))+".txt", []byte("data"), 0644); err != nil {
 			t.Fatal(err)
 		}
 	}
-	
+
 	// Run 100 scans
 	for i := 0; i < 100; i++ {
 		_, err := worker.ScanArtifactsNative(tmpDir)
 		if err != nil {
 			t.Logf("Scan %d: %v (may be expected if native disabled)", i, err)
 		}
-		
+
 		if i%25 == 0 {
 			t.Logf("Completed %d scans", i)
 		}
diff --git a/tests/benchmarks/native_queue_bench_test.go b/tests/benchmarks/native_queue_bench_test.go
index fa0aeae..6b7652d 100644
--- a/tests/benchmarks/native_queue_bench_test.go
+++ b/tests/benchmarks/native_queue_bench_test.go
@@ -10,6 +10,10 @@ import (
 // Tier 1 C++ candidate: binary format vs JSON
 // Expected: 5x speedup, 99% allocation reduction
 func BenchmarkNativeQueueRebuildIndex(b *testing.B) {
+	if !queue.UseNativeQueue {
+		b.Skip("Native queue not enabled (set FETCHML_NATIVE_LIBS=1 or build with -tags native_libs)")
+	}
+
 	tmpDir := b.TempDir()
 	q, err := queue.NewNativeQueue(tmpDir)
 	if err != nil {
@@ -47,6 +51,10 @@ func BenchmarkNativeQueueRebuildIndex(b *testing.B) {
 
 // BenchmarkNativeQueueClaimNext profiles task claiming from binary heap
 func BenchmarkNativeQueueClaimNext(b *testing.B) {
+	if !queue.UseNativeQueue {
+		b.Skip("Native queue not enabled (set FETCHML_NATIVE_LIBS=1 or build with -tags native_libs)")
+	}
+
 	tmpDir := b.TempDir()
 	q, err := queue.NewNativeQueue(tmpDir)
 	if err != nil {
@@ -77,6 +85,10 @@ func BenchmarkNativeQueueClaimNext(b *testing.B) {
 
 // BenchmarkNativeQueueGetAllTasks profiles full task scan from binary index
 func BenchmarkNativeQueueGetAllTasks(b *testing.B) {
+	if !queue.UseNativeQueue {
+		b.Skip("Native queue not enabled (set FETCHML_NATIVE_LIBS=1 or build with -tags native_libs)")
+	}
+
 	tmpDir := b.TempDir()
 	q, err := queue.NewNativeQueue(tmpDir)
 	if err != nil {
diff --git a/tests/benchmarks/queue_bench_test.go b/tests/benchmarks/queue_bench_test.go
index 59f9b7d..640371c 100644
--- a/tests/benchmarks/queue_bench_test.go
+++ b/tests/benchmarks/queue_bench_test.go
@@ -1,3 +1,6 @@
+//go:build !native_libs
+// +build !native_libs
+
 package benchmarks
 
 import (