diff --git a/docs/changelog/123010.yaml b/docs/changelog/123010.yaml
new file mode 100644
index 0000000000000..3d95d775b8a54
--- /dev/null
+++ b/docs/changelog/123010.yaml
@@ -0,0 +1,6 @@
+pr: 123010
+summary: Hold store reference in `InternalEngine#performActionWithDirectoryReader(...)`
+area: Engine
+type: bug
+issues:
+ - 122974
diff --git a/muted-tests.yml b/muted-tests.yml
index e8502b52a3464..9a8be7e0241fe 100644
--- a/muted-tests.yml
+++ b/muted-tests.yml
@@ -314,9 +314,6 @@ tests:
   issue: https://github.com/elastic/elasticsearch/issues/122913
 - class: org.elasticsearch.xpack.search.AsyncSearchSecurityIT
   issue: https://github.com/elastic/elasticsearch/issues/122940
-- class: org.elasticsearch.action.admin.indices.create.ShrinkIndexIT
-  method: testShrinkIndexPrimaryTerm
-  issue: https://github.com/elastic/elasticsearch/issues/122974
 - class: org.elasticsearch.test.apmintegration.TracesApmIT
   method: testApmIntegration
   issue: https://github.com/elastic/elasticsearch/issues/122129
diff --git a/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java b/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
index 94e8989bc5a1c..fc7f6eab0856c 100644
--- a/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
+++ b/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
@@ -3470,7 +3470,9 @@ protected long getPreCommitSegmentGeneration() {
     <T> T performActionWithDirectoryReader(SearcherScope scope, CheckedFunction<DirectoryReader, T, IOException> action)
         throws EngineException {
         assert scope == SearcherScope.INTERNAL : "performActionWithDirectoryReader(...) isn't prepared for external usage";
-        assert store.hasReferences();
+        if (store.tryIncRef() == false) {
+            throw new AlreadyClosedException(shardId + " store is closed", failedEngine.get());
+        }
         try {
             ReferenceManager<ElasticsearchDirectoryReader> referenceManager = getReferenceManager(scope);
             ElasticsearchDirectoryReader acquire = referenceManager.acquire();
@@ -3486,6 +3488,8 @@ <T> T performActionWithDirectoryReader(SearcherScope scope, CheckedFunction<Dire
             ensureOpen(ex); // throw EngineCloseException here if we are already closed
             logger.error("failed to perform action with directory reader", ex);
             throw new EngineException(shardId, "failed to perform action with directory reader", ex);
+        } finally {
+            store.decRef();
         }
     }
 }