diff --git a/hudi-common/src/main/java/org/apache/hudi/common/bootstrap/index/HFileBootstrapIndex.java b/hudi-common/src/main/java/org/apache/hudi/common/bootstrap/index/HFileBootstrapIndex.java
index b8a2c202cb6c..718fff3cf3a7 100644
--- a/hudi-common/src/main/java/org/apache/hudi/common/bootstrap/index/HFileBootstrapIndex.java
+++ b/hudi-common/src/main/java/org/apache/hudi/common/bootstrap/index/HFileBootstrapIndex.java
@@ -34,6 +34,7 @@
 import org.apache.hudi.exception.HoodieException;
 import org.apache.hudi.exception.HoodieIOException;
 import org.apache.hudi.io.storage.HoodieHFileUtils;
+import org.apache.hudi.metadata.HoodieTableMetadata;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
@@ -101,7 +102,10 @@ public HFileBootstrapIndex(HoodieTableMetaClient metaClient) {
     Path indexByFilePath = fileIdIndexPath(metaClient);
     try {
       FileSystem fs = metaClient.getFs();
-      isPresent = fs.exists(indexByPartitionPath) && fs.exists(indexByFilePath);
+      // The metadata table is never bootstrapped, so the bootstrap index is always absent
+      // for the metadata table.  The fs.exists calls are avoided for metadata table.
+      isPresent = !HoodieTableMetadata.isMetadataTable(metaClient.getBasePathV2().toString())
+          && fs.exists(indexByPartitionPath) && fs.exists(indexByFilePath);
     } catch (IOException ioe) {
       throw new HoodieIOException(ioe.getMessage(), ioe);
     }