diff --git a/server/src/main/java/org/elasticsearch/gateway/MetaStateService.java b/server/src/main/java/org/elasticsearch/gateway/MetaStateService.java
index 3bd8ba11a57ec..3ce3f8918a190 100644
--- a/server/src/main/java/org/elasticsearch/gateway/MetaStateService.java
+++ b/server/src/main/java/org/elasticsearch/gateway/MetaStateService.java
@@ -21,6 +21,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.elasticsearch.cluster.metadata.IndexGraveyard;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
 import org.elasticsearch.cluster.metadata.Manifest;
 import org.elasticsearch.cluster.metadata.MetaData;
@@ -115,12 +116,15 @@ private Tuple<Manifest, MetaData> loadFullStateBWC() throws IOException {
         MetaData globalMetaData = metaDataAndGeneration.v1();
         long globalStateGeneration = metaDataAndGeneration.v2();
 
+        final IndexGraveyard indexGraveyard;
         if (globalMetaData != null) {
             metaDataBuilder = MetaData.builder(globalMetaData);
+            indexGraveyard = globalMetaData.custom(IndexGraveyard.TYPE);
             // TODO https://github.com/elastic/elasticsearch/issues/38556
             // assert Version.CURRENT.major < 8 : "failed to find manifest file, which is mandatory staring with Elasticsearch version 8.0";
         } else {
             metaDataBuilder = MetaData.builder();
+            indexGraveyard = IndexGraveyard.builder().build();
         }
 
         for (String indexFolderName : nodeEnv.availableIndexFolders()) {
@@ -132,8 +136,13 @@ private Tuple<Manifest, MetaData> loadFullStateBWC() throws IOException {
             IndexMetaData indexMetaData = indexMetaDataAndGeneration.v1();
             long generation = indexMetaDataAndGeneration.v2();
             if (indexMetaData != null) {
-                indices.put(indexMetaData.getIndex(), generation);
-                metaDataBuilder.put(indexMetaData, false);
+                if (indexGraveyard.containsIndex(indexMetaData.getIndex())) {
+                    logger.debug("[{}] found metadata for deleted index [{}]", indexFolderName, indexMetaData.getIndex());
+                    // this index folder is cleared up when state is recovered
+                } else {
+                    indices.put(indexMetaData.getIndex(), generation);
+                    metaDataBuilder.put(indexMetaData, false);
+                }
             } else {
                 logger.debug("[{}] failed to find metadata for existing index location", indexFolderName);
             }
diff --git a/server/src/test/java/org/elasticsearch/gateway/GatewayIndexStateIT.java b/server/src/test/java/org/elasticsearch/gateway/GatewayIndexStateIT.java
index e9cbd912202a0..1df326cb1857e 100644
--- a/server/src/test/java/org/elasticsearch/gateway/GatewayIndexStateIT.java
+++ b/server/src/test/java/org/elasticsearch/gateway/GatewayIndexStateIT.java
@@ -30,8 +30,10 @@
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.Requests;
 import org.elasticsearch.cluster.ClusterState;
+import org.elasticsearch.cluster.coordination.CoordinationMetaData;
 import org.elasticsearch.cluster.metadata.IndexGraveyard;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
+import org.elasticsearch.cluster.metadata.Manifest;
 import org.elasticsearch.cluster.metadata.MappingMetaData;
 import org.elasticsearch.cluster.metadata.MetaData;
 import org.elasticsearch.cluster.routing.IndexRoutingTable;
@@ -39,11 +41,13 @@
 import org.elasticsearch.cluster.routing.RoutingTable;
 import org.elasticsearch.cluster.routing.ShardRoutingState;
 import org.elasticsearch.cluster.routing.UnassignedInfo;
+import org.elasticsearch.cluster.service.ClusterService;
 import org.elasticsearch.common.CheckedConsumer;
 import org.elasticsearch.common.Priority;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.xcontent.XContentFactory;
 import org.elasticsearch.common.xcontent.XContentType;
+import org.elasticsearch.core.internal.io.IOUtils;
 import org.elasticsearch.env.NodeEnvironment;
 import org.elasticsearch.index.mapper.MapperParsingException;
 import org.elasticsearch.indices.IndexClosedException;
@@ -54,6 +58,8 @@
 import org.elasticsearch.test.InternalTestCluster.RestartCallback;
 
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.TimeUnit;
@@ -66,6 +72,7 @@
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertAcked;
 import static org.elasticsearch.test.hamcrest.ElasticsearchAssertions.assertHitCount;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.notNullValue;
@@ -508,6 +515,42 @@ public void testArchiveBrokenClusterSettings() throws Exception {
         assertHitCount(client().prepareSearch().setQuery(matchAllQuery()).get(), 1L);
     }
 
+    public void testHalfDeletedIndexImport() throws Exception {
+        // It's possible for a 6.x node to add a tombstone for an index but not actually delete the index metadata from disk since that
+        // deletion is slightly deferred and may race against the node being shut down; if you upgrade to 7.x when in this state then the
+        // node won't start.
+
+        internalCluster().startNode();
+        createIndex("test", Settings.builder()
+            .put(IndexMetaData.SETTING_NUMBER_OF_SHARDS, 1)
+            .put(IndexMetaData.SETTING_NUMBER_OF_REPLICAS, 0)
+            .build());
+        ensureGreen("test");
+
+        final MetaData metaData = internalCluster().getInstance(ClusterService.class).state().metaData();
+        final Path[] paths = internalCluster().getInstance(NodeEnvironment.class).nodeDataPaths();
+        writeBrokenMeta(metaStateService -> {
+            metaStateService.writeGlobalState("test", MetaData.builder(metaData)
+                // we remove the manifest file, resetting the term and making this look like an upgrade from 6.x, so must also reset the
+                // term in the coordination metadata
+                .coordinationMetaData(CoordinationMetaData.builder(metaData.coordinationMetaData()).term(0L).build())
+                // add a tombstone but do not delete the index metadata from disk
+                .putCustom(IndexGraveyard.TYPE, IndexGraveyard.builder().addTombstone(metaData.index("test").getIndex()).build()).build());
+            for (final Path path : paths) {
+                try (Stream<Path> stateFiles = Files.list(path.resolve(MetaDataStateFormat.STATE_DIR_NAME))) {
+                    for (final Path manifestPath : stateFiles
+                        .filter(p -> p.getFileName().toString().startsWith(Manifest.FORMAT.getPrefix())).collect(Collectors.toList())) {
+                        IOUtils.rm(manifestPath);
+                    }
+                }
+            }
+        });
+
+        ensureGreen();
+
+        assertBusy(() -> assertThat(internalCluster().getInstance(NodeEnvironment.class).availableIndexFolders(), empty()));
+    }
+
     private void writeBrokenMeta(CheckedConsumer<MetaStateService, IOException> writer) throws Exception {
         Map<String, MetaStateService> metaStateServices = Stream.of(internalCluster().getNodeNames())
             .collect(Collectors.toMap(Function.identity(), nodeName -> internalCluster().getInstance(MetaStateService.class, nodeName)));