diff --git a/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java b/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java
index 2febef58d54..f5d17eca036 100644
--- a/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java
+++ b/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java
@@ -58,6 +58,7 @@ import org.elasticsearch.common.metrics.CounterMetric;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.ByteSizeValue;
+import org.elasticsearch.common.util.set.Sets;
 import org.elasticsearch.common.xcontent.LoggingDeprecationHandler;
 import org.elasticsearch.common.xcontent.NamedXContentRegistry;
 import org.elasticsearch.common.xcontent.XContentFactory;
@@ -100,6 +101,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -433,9 +435,10 @@ public abstract class BlobStoreRepository extends AbstractLifecycleComponent imp
                 return;
             }
             final SnapshotInfo finalSnapshotInfo = snapshot;
+            final List<String> snapMetaFilesToDelete =
+                Arrays.asList(snapshotFormat.blobName(snapshotId.getUUID()), globalMetaDataFormat.blobName(snapshotId.getUUID()));
             try {
-                blobContainer().deleteBlobsIgnoringIfNotExists(
-                    Arrays.asList(snapshotFormat.blobName(snapshotId.getUUID()), globalMetaDataFormat.blobName(snapshotId.getUUID())));
+                blobContainer().deleteBlobsIgnoringIfNotExists(snapMetaFilesToDelete);
             } catch (IOException e) {
                 logger.warn(() -> new ParameterizedMessage("[{}] Unable to delete global metadata files", snapshotId), e);
             }
@@ -448,12 +451,56 @@ public abstract class BlobStoreRepository extends AbstractLifecycleComponent imp
                 snapshotId,
                 ActionListener.map(listener, v -> {
                     cleanupStaleIndices(foundIndices, survivingIndices);
+                    cleanupStaleRootFiles(Sets.difference(rootBlobs, new HashSet<>(snapMetaFilesToDelete)), updatedRepositoryData);
                     return null;
                 })
             );
         }
     }
 
+    private void cleanupStaleRootFiles(Set<String> rootBlobNames, RepositoryData repositoryData) {
+        final Set<String> allSnapshotIds =
+            repositoryData.getAllSnapshotIds().stream().map(SnapshotId::getUUID).collect(Collectors.toSet());
+        final List<String> blobsToDelete = rootBlobNames.stream().filter(
+            blob -> {
+                if (FsBlobContainer.isTempBlobName(blob)) {
+                    return true;
+                }
+                if (blob.endsWith(".dat")) {
+                    final String foundUUID;
+                    if (blob.startsWith(SNAPSHOT_PREFIX)) {
+                        foundUUID = blob.substring(SNAPSHOT_PREFIX.length(), blob.length() - ".dat".length());
+                        assert snapshotFormat.blobName(foundUUID).equals(blob);
+                    } else if (blob.startsWith(METADATA_PREFIX)) {
+                        foundUUID = blob.substring(METADATA_PREFIX.length(), blob.length() - ".dat".length());
+                        assert globalMetaDataFormat.blobName(foundUUID).equals(blob);
+                    } else {
+                        return false;
+                    }
+                    return allSnapshotIds.contains(foundUUID) == false;
+                }
+                return false;
+            }
+        ).collect(Collectors.toList());
+        if (blobsToDelete.isEmpty()) {
+            return;
+        }
+        try {
+            logger.info("[{}] Found stale root level blobs {}. Cleaning them up", metadata.name(), blobsToDelete);
+            blobContainer().deleteBlobsIgnoringIfNotExists(blobsToDelete);
+        } catch (IOException e) {
+            logger.warn(() -> new ParameterizedMessage(
+                "[{}] The following blobs are no longer part of any snapshot [{}] but failed to remove them",
+                metadata.name(), blobsToDelete), e);
+        } catch (Exception e) {
+            // TODO: We shouldn't be blanket catching and suppressing all exceptions here and instead handle them safely upstream.
+            //       Currently this catch exists as a stop gap solution to tackle unexpected runtime exceptions from implementations
+            //       bubbling up and breaking the snapshot functionality.
+            assert false : e;
+            logger.warn(new ParameterizedMessage("[{}] Exception during cleanup of root level blobs", metadata.name()), e);
+        }
+    }
+
     private void cleanupStaleIndices(Map<String, BlobContainer> foundIndices, Map<String, IndexId> survivingIndices) {
         try {
             final Set<String> survivingIndexIds = survivingIndices.values().stream()
diff --git a/test/framework/src/main/java/org/elasticsearch/repositories/AbstractThirdPartyRepositoryTestCase.java b/test/framework/src/main/java/org/elasticsearch/repositories/AbstractThirdPartyRepositoryTestCase.java
index e32c3945673..62d2e50cef8 100644
--- a/test/framework/src/main/java/org/elasticsearch/repositories/AbstractThirdPartyRepositoryTestCase.java
+++ b/test/framework/src/main/java/org/elasticsearch/repositories/AbstractThirdPartyRepositoryTestCase.java
@@ -236,6 +236,10 @@ public abstract class AbstractThirdPartyRepositoryTestCase extends ESSingleNodeT
                 final BlobStore blobStore = repo.blobStore();
                 blobStore.blobContainer(BlobPath.cleanPath().add("indices").add("foo"))
                     .writeBlob("bar", new ByteArrayInputStream(new byte[0]), 0, false);
+                for (String prefix : Arrays.asList("snap-", "meta-")) {
+                    blobStore.blobContainer(BlobPath.cleanPath())
+                        .writeBlob(prefix + "foo.dat", new ByteArrayInputStream(new byte[0]), 0, false);
+                }
                 future.onResponse(null);
             }
         });
@@ -256,6 +260,8 @@ public abstract class AbstractThirdPartyRepositoryTestCase extends ESSingleNodeT
                 future.onResponse(
                     blobStore.blobContainer(BlobPath.cleanPath().add("indices")).children().containsKey("foo")
                         && blobStore.blobContainer(BlobPath.cleanPath().add("indices").add("foo")).blobExists("bar")
+                        && blobStore.blobContainer(BlobPath.cleanPath()).blobExists("meta-foo.dat")
+                        && blobStore.blobContainer(BlobPath.cleanPath()).blobExists("snap-foo.dat")
                 );
             }
         });