diff --git a/backends-velox/src/main/scala/io/glutenproject/backendsapi/velox/VeloxBackend.scala b/backends-velox/src/main/scala/io/glutenproject/backendsapi/velox/VeloxBackend.scala
index beee871bc0ef2..906cc4db741d5 100644
--- a/backends-velox/src/main/scala/io/glutenproject/backendsapi/velox/VeloxBackend.scala
+++ b/backends-velox/src/main/scala/io/glutenproject/backendsapi/velox/VeloxBackend.scala
@@ -110,6 +110,8 @@ object BackendSettings extends BackendSettingsApi {
     }
   }
 
+  override def supportNativeMetadataColumns(): Boolean = true
+
   override def supportExpandExec(): Boolean = true
 
   override def supportSortExec(): Boolean = true
diff --git a/gluten-core/src/main/scala/io/glutenproject/backendsapi/BackendSettingsApi.scala b/gluten-core/src/main/scala/io/glutenproject/backendsapi/BackendSettingsApi.scala
index fcd1bbfe84533..4654dd43daffb 100644
--- a/gluten-core/src/main/scala/io/glutenproject/backendsapi/BackendSettingsApi.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/backendsapi/BackendSettingsApi.scala
@@ -34,6 +34,7 @@ trait BackendSettingsApi {
       fields: Array[StructField],
       partTable: Boolean,
       paths: Seq[String]): Boolean = false
+  def supportNativeMetadataColumns(): Boolean = false
   def supportExpandExec(): Boolean = false
   def supportSortExec(): Boolean = false
   def supportSortMergeJoinExec(): Boolean = true
diff --git a/gluten-core/src/main/scala/io/glutenproject/execution/FileSourceScanExecTransformer.scala b/gluten-core/src/main/scala/io/glutenproject/execution/FileSourceScanExecTransformer.scala
index 2a9bd9c176ae2..f7a42dfa2046a 100644
--- a/gluten-core/src/main/scala/io/glutenproject/execution/FileSourceScanExecTransformer.scala
+++ b/gluten-core/src/main/scala/io/glutenproject/execution/FileSourceScanExecTransformer.scala
@@ -116,6 +116,12 @@ class FileSourceScanExecTransformer(
   override def hashCode(): Int = super.hashCode()
 
   override protected def doValidateInternal(): ValidationResult = {
+    if (
+      !metadataColumns.isEmpty && !BackendsApiManager.getSettings.supportNativeMetadataColumns()
+    ) {
+      return ValidationResult.notOk(s"Unsupported metadata columns scan in native.")
+    }
+
     if (hasUnsupportedColumns) {
       return ValidationResult.notOk(s"Unsupported columns scan in native.")
     }