diff --git a/server/src/internalClusterTest/java/org/elasticsearch/snapshots/DedicatedClusterSnapshotRestoreIT.java b/server/src/internalClusterTest/java/org/elasticsearch/snapshots/DedicatedClusterSnapshotRestoreIT.java
index 08868bbb330c4..9db06316e942c 100644
--- a/server/src/internalClusterTest/java/org/elasticsearch/snapshots/DedicatedClusterSnapshotRestoreIT.java
+++ b/server/src/internalClusterTest/java/org/elasticsearch/snapshots/DedicatedClusterSnapshotRestoreIT.java
@@ -11,6 +11,9 @@
 import com.carrotsearch.hppc.IntHashSet;
 import com.carrotsearch.hppc.IntSet;
 
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.elasticsearch.action.ActionFuture;
 import org.elasticsearch.action.ActionListener;
 import org.elasticsearch.action.admin.cluster.snapshots.create.CreateSnapshotRequest;
@@ -33,6 +36,7 @@
 import org.elasticsearch.cluster.node.DiscoveryNode;
 import org.elasticsearch.common.Priority;
 import org.elasticsearch.common.Strings;
+import org.elasticsearch.common.logging.Loggers;
 import org.elasticsearch.common.network.CloseableChannel;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.settings.SettingsFilter;
@@ -59,6 +63,7 @@
 import org.elasticsearch.test.ESIntegTestCase.ClusterScope;
 import org.elasticsearch.test.ESIntegTestCase.Scope;
 import org.elasticsearch.test.InternalTestCluster;
+import org.elasticsearch.test.MockLogAppender;
 import org.elasticsearch.test.disruption.BusyMasterServiceDisruption;
 import org.elasticsearch.test.disruption.ServiceDisruptionScheme;
 import org.elasticsearch.test.rest.FakeRestRequest;
@@ -1305,6 +1310,38 @@ public void testConcurrentSnapshotAndRepoDelete() throws Exception {
         }
     }
 
+    public void testDeleteSnapshotsOfDifferentIndexSets() throws IllegalAccessException {
+        internalCluster().startMasterOnlyNodes(1);
+        internalCluster().startDataOnlyNode();
+        final String repoName = "test-repo";
+        createRepository(repoName, "fs");
+
+        final MockLogAppender mockAppender = new MockLogAppender();
+        mockAppender.addExpectation(
+            new MockLogAppender.UnseenEventExpectation("no warnings", BlobStoreRepository.class.getCanonicalName(), Level.WARN, "*")
+        );
+        mockAppender.start();
+        final Logger logger = LogManager.getLogger(BlobStoreRepository.class);
+        Loggers.addAppender(logger, mockAppender);
+        try {
+            final String index1 = "index-1";
+            final String index2 = "index-2";
+            createIndexWithContent("index-1");
+            createIndexWithContent("index-2");
+            createFullSnapshot(repoName, "full-snapshot");
+            final String snapshot1 = "index-1-snapshot";
+            final String snapshot2 = "index-2-snapshot";
+            createSnapshot(repoName, snapshot1, org.elasticsearch.core.List.of(index1));
+            createSnapshot(repoName, snapshot2, org.elasticsearch.core.List.of(index2));
+
+            clusterAdmin().prepareDeleteSnapshot(repoName, snapshot1, snapshot2).get();
+            mockAppender.assertAllExpectationsMatched();
+        } finally {
+            Loggers.removeAppender(logger, mockAppender);
+            mockAppender.stop();
+        }
+    }
+
     private long calculateTotalFilesSize(List<Path> files) {
         return files.stream().mapToLong(f -> {
             try {
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 5004171052d24..03260958106aa 100644
--- a/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java
+++ b/server/src/main/java/org/elasticsearch/repositories/blobstore/BlobStoreRepository.java
@@ -1004,12 +1004,13 @@ private void writeUpdatedShardMetaDataAndComputeDeletes(
         );
 
         for (IndexId indexId : indices) {
-            final Set<SnapshotId> survivingSnapshots = oldRepositoryData.getSnapshots(indexId)
-                .stream()
+            final Set<SnapshotId> snapshotsWithIndex = org.elasticsearch.core.Set.copyOf(oldRepositoryData.getSnapshots(indexId));
+            final Set<SnapshotId> survivingSnapshots = snapshotsWithIndex.stream()
                 .filter(id -> snapshotIds.contains(id) == false)
                 .collect(Collectors.toSet());
             final StepListener<Collection<Integer>> shardCountListener = new StepListener<>();
             final Collection<String> indexMetaGenerations = snapshotIds.stream()
+                .filter(snapshotsWithIndex::contains)
                 .map(id -> oldRepositoryData.indexMetaDataGenerations().indexMetaBlobId(id, indexId))
                 .collect(Collectors.toSet());
             final ActionListener<Integer> allShardCountsListener = new GroupedActionListener<>(