diff --git a/hudi-client/hudi-client-common/src/main/java/org/apache/hudi/metadata/HoodieBackedTableMetadataWriter.java b/hudi-client/hudi-client-common/src/main/java/org/apache/hudi/metadata/HoodieBackedTableMetadataWriter.java
index 1f76a5e30b803..bf7af4305a796 100644
--- a/hudi-client/hudi-client-common/src/main/java/org/apache/hudi/metadata/HoodieBackedTableMetadataWriter.java
+++ b/hudi-client/hudi-client-common/src/main/java/org/apache/hudi/metadata/HoodieBackedTableMetadataWriter.java
@@ -316,6 +316,7 @@ private Map<String, List<FileStatus>> getPartitionsToFilesMapping(HoodieTableMet
     Map<String, List<FileStatus>> partitionToFileStatus = new HashMap<>();
     final int fileListingParallelism = metadataWriteConfig.getFileListingParallelism();
     SerializableConfiguration conf = new SerializableConfiguration(datasetMetaClient.getHadoopConf());
+    final String dirFilterRegex = datasetWriteConfig.getMetadataConfig().getDirectoryFilterRegex();
 
     while (!pathsToList.isEmpty()) {
       int listingParallelism = Math.min(fileListingParallelism, pathsToList.size());
@@ -329,6 +330,11 @@ private Map<String, List<FileStatus>> getPartitionsToFilesMapping(HoodieTableMet
       // If the listing reveals a directory, add it to queue. If the listing reveals a hoodie partition, add it to
       // the results.
       dirToFileListing.forEach(p -> {
+        if (!dirFilterRegex.isEmpty() && p.getLeft().getName().matches(dirFilterRegex)) {
+          LOG.info("Ignoring directory " + p.getLeft() + " which matches the filter regex " + dirFilterRegex);
+          return;
+        }
+
         List<FileStatus> filesInDir = Arrays.stream(p.getRight()).parallel()
             .filter(fs -> !fs.getPath().getName().equals(HoodiePartitionMetadata.HOODIE_PARTITION_METAFILE))
             .collect(Collectors.toList());
diff --git a/hudi-client/hudi-spark-client/src/test/java/org/apache/hudi/metadata/TestHoodieBackedMetadata.java b/hudi-client/hudi-spark-client/src/test/java/org/apache/hudi/metadata/TestHoodieBackedMetadata.java
index c238fc04b84bb..105d4d99bf79e 100644
--- a/hudi-client/hudi-spark-client/src/test/java/org/apache/hudi/metadata/TestHoodieBackedMetadata.java
+++ b/hudi-client/hudi-spark-client/src/test/java/org/apache/hudi/metadata/TestHoodieBackedMetadata.java
@@ -149,14 +149,22 @@ public void testOnlyValidPartitionsAdded() throws Exception {
     final String nonPartitionDirectory = HoodieTestDataGenerator.DEFAULT_PARTITION_PATHS[0] + "-nonpartition";
     Files.createDirectories(Paths.get(basePath, nonPartitionDirectory));
 
+    // Three directories which are partitions but will be ignored due to filter
+    final String filterDirRegex = ".*-filterDir\\d|\\..*";
+    final String filteredDirectoryOne = HoodieTestDataGenerator.DEFAULT_PARTITION_PATHS[0] + "-filterDir1";
+    final String filteredDirectoryTwo = HoodieTestDataGenerator.DEFAULT_PARTITION_PATHS[0] + "-filterDir2";
+    final String filteredDirectoryThree = ".backups";
+
     // Create some commits
     HoodieTestTable testTable = HoodieTestTable.of(metaClient);
-    testTable.withPartitionMetaFiles("p1", "p2")
+    testTable.withPartitionMetaFiles("p1", "p2", filteredDirectoryOne, filteredDirectoryTwo, filteredDirectoryThree)
         .addCommit("001").withBaseFilesInPartition("p1", 10).withBaseFilesInPartition("p2", 10, 10)
         .addCommit("002").withBaseFilesInPartition("p1", 10).withBaseFilesInPartition("p2", 10, 10, 10)
         .addInflightCommit("003").withBaseFilesInPartition("p1", 10).withBaseFilesInPartition("p2", 10);
 
-    try (SparkRDDWriteClient client = new SparkRDDWriteClient(engineContext, getWriteConfig(true, true))) {
+    final HoodieWriteConfig writeConfig = getWriteConfigBuilder(true, true, false)
+        .withMetadataConfig(HoodieMetadataConfig.newBuilder().enable(true).withDirectoryFilterRegex(filterDirRegex).build()).build();
+    try (SparkRDDWriteClient client = new SparkRDDWriteClient(engineContext, writeConfig)) {
       client.startCommitWithTime("005");
 
       List<String> partitions = metadataWriter(client).metadata().getAllPartitionPaths();
@@ -165,6 +173,13 @@ public void testOnlyValidPartitionsAdded() throws Exception {
       assertTrue(partitions.contains("p1"), "Must contain partition p1");
       assertTrue(partitions.contains("p2"), "Must contain partition p2");
 
+      assertFalse(partitions.contains(filteredDirectoryOne),
+          "Must not contain the filtered directory " + filteredDirectoryOne);
+      assertFalse(partitions.contains(filteredDirectoryTwo),
+          "Must not contain the filtered directory " + filteredDirectoryTwo);
+      assertFalse(partitions.contains(filteredDirectoryThree),
+          "Must not contain the filtered directory " + filteredDirectoryThree);
+
       FileStatus[] statuses = metadata(client).getAllFilesInPartition(new Path(basePath, "p1"));
       assertTrue(statuses.length == 2);
       statuses = metadata(client).getAllFilesInPartition(new Path(basePath, "p2"));
diff --git a/hudi-common/src/main/java/org/apache/hudi/common/config/HoodieMetadataConfig.java b/hudi-common/src/main/java/org/apache/hudi/common/config/HoodieMetadataConfig.java
index 1ead9c8dc28f7..6346a65fb88f8 100644
--- a/hudi-common/src/main/java/org/apache/hudi/common/config/HoodieMetadataConfig.java
+++ b/hudi-common/src/main/java/org/apache/hudi/common/config/HoodieMetadataConfig.java
@@ -75,6 +75,10 @@ public final class HoodieMetadataConfig extends DefaultHoodieConfig {
   public static final String ENABLE_FALLBACK_PROP = METADATA_PREFIX + ".fallback.enable";
   public static final String DEFAULT_ENABLE_FALLBACK = "true";
 
+  // Regex to filter out matching directories during bootstrap
+  public static final String DIRECTORY_FILTER_REGEX = METADATA_PREFIX + ".dir.filter.regex";
+  public static final String DEFAULT_DIRECTORY_FILTER_REGEX = "";
+
   public static final String HOODIE_ASSUME_DATE_PARTITIONING_PROP = "hoodie.assume.date.partitioning";
   public static final String DEFAULT_ASSUME_DATE_PARTITIONING = "false";
 
@@ -117,6 +121,10 @@ public boolean enableMetrics() {
     return Boolean.parseBoolean(props.getProperty(METADATA_METRICS_ENABLE_PROP));
   }
 
+  public String getDirectoryFilterRegex() {
+    return props.getProperty(DIRECTORY_FILTER_REGEX);
+  }
+
   public static class Builder {
 
     private final Properties props = new Properties();
@@ -194,6 +202,11 @@ public Builder withAssumeDatePartitioning(boolean assumeDatePartitioning) {
       return this;
     }
 
+    public Builder withDirectoryFilterRegex(String regex) {
+      props.setProperty(DIRECTORY_FILTER_REGEX, regex);
+      return this;
+    }
+
     public HoodieMetadataConfig build() {
       HoodieMetadataConfig config = new HoodieMetadataConfig(props);
       setDefaultOnCondition(props, !props.containsKey(METADATA_ENABLE_PROP), METADATA_ENABLE_PROP,
@@ -222,6 +235,8 @@ public HoodieMetadataConfig build() {
           DEFAULT_ENABLE_FALLBACK);
       setDefaultOnCondition(props, !props.containsKey(ENABLE_REUSE_PROP), ENABLE_REUSE_PROP,
           DEFAULT_ENABLE_REUSE);
+      setDefaultOnCondition(props, !props.containsKey(DIRECTORY_FILTER_REGEX), DIRECTORY_FILTER_REGEX,
+          DEFAULT_DIRECTORY_FILTER_REGEX);
       return config;
     }
   }