diff --git a/CHANGELOG.md b/CHANGELOG.md
index de832cdc5c52f..f44c993f6faa0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -107,6 +107,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Add a counter to node stat api to track shard going from idle to non-idle ([#12768](https://github.com/opensearch-project/OpenSearch/pull/12768))
 - Allow setting KEYSTORE_PASSWORD through env variable ([#12865](https://github.com/opensearch-project/OpenSearch/pull/12865))
 - [Concurrent Segment Search] Perform buildAggregation concurrently and support Composite Aggregations ([#12697](https://github.com/opensearch-project/OpenSearch/pull/12697))
+- [Concurrent Segment Search] Disable concurrent segment search for system indices and throttled requests ([#12954](https://github.com/opensearch-project/OpenSearch/pull/12954))
 
 ### Dependencies
 - Bump `org.apache.commons:commons-configuration2` from 2.10.0 to 2.10.1 ([#12896](https://github.com/opensearch-project/OpenSearch/pull/12896))
diff --git a/server/src/main/java/org/opensearch/search/DefaultSearchContext.java b/server/src/main/java/org/opensearch/search/DefaultSearchContext.java
index 061aa2f6e5896..c76ea71c0a094 100644
--- a/server/src/main/java/org/opensearch/search/DefaultSearchContext.java
+++ b/server/src/main/java/org/opensearch/search/DefaultSearchContext.java
@@ -962,6 +962,12 @@ public BucketCollectorProcessor bucketCollectorProcessor() {
      *         false: otherwise
      */
     private boolean evaluateConcurrentSegmentSearchSettings(Executor concurrentSearchExecutor) {
+        // Do not use concurrent segment search for system indices or throttled requests. See:
+        // https://github.com/opensearch-project/OpenSearch/issues/12951
+        if (indexShard.isSystem() || indexShard.indexSettings().isSearchThrottled()) {
+            return false;
+        }
+
         if ((clusterService != null) && (concurrentSearchExecutor != null)) {
             return indexService.getIndexSettings()
                 .getSettings()
@@ -969,9 +975,8 @@ private boolean evaluateConcurrentSegmentSearchSettings(Executor concurrentSearc
                     IndexSettings.INDEX_CONCURRENT_SEGMENT_SEARCH_SETTING.getKey(),
                     clusterService.getClusterSettings().get(CLUSTER_CONCURRENT_SEGMENT_SEARCH_SETTING)
                 );
-        } else {
-            return false;
         }
+        return false;
     }
 
     @Override
diff --git a/server/src/test/java/org/opensearch/search/DefaultSearchContextTests.java b/server/src/test/java/org/opensearch/search/DefaultSearchContextTests.java
index 3793249d569f0..a1a808c9faa9b 100644
--- a/server/src/test/java/org/opensearch/search/DefaultSearchContextTests.java
+++ b/server/src/test/java/org/opensearch/search/DefaultSearchContextTests.java
@@ -93,6 +93,7 @@
 import java.util.function.Function;
 import java.util.function.Supplier;
 
+import static org.opensearch.index.IndexSettings.INDEX_SEARCH_THROTTLED;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.is;
 import static org.mockito.Mockito.any;
@@ -168,6 +169,7 @@ public void testPreProcess() throws Exception {
         IndexSettings indexSettings = new IndexSettings(indexMetadata, Settings.EMPTY);
         when(indexService.getIndexSettings()).thenReturn(indexSettings);
         when(mapperService.getIndexSettings()).thenReturn(indexSettings);
+        when(indexShard.indexSettings()).thenReturn(indexSettings);
 
         BigArrays bigArrays = new MockBigArrays(new MockPageCacheRecycler(Settings.EMPTY), new NoneCircuitBreakerService());
 
@@ -486,6 +488,14 @@ public void testClearQueryCancellationsOnClose() throws IOException {
         when(indexService.newQueryShardContext(eq(shardId.id()), any(), any(), nullable(String.class), anyBoolean())).thenReturn(
             queryShardContext
         );
+        Settings settings = Settings.builder()
+            .put(IndexMetadata.SETTING_VERSION_CREATED, Version.CURRENT)
+            .put(IndexMetadata.SETTING_NUMBER_OF_REPLICAS, 1)
+            .put(IndexMetadata.SETTING_NUMBER_OF_SHARDS, 2)
+            .build();
+        IndexMetadata indexMetadata = IndexMetadata.builder("index").settings(settings).build();
+        IndexSettings indexSettings = new IndexSettings(indexMetadata, Settings.EMPTY);
+        when(indexShard.indexSettings()).thenReturn(indexSettings);
 
         BigArrays bigArrays = new MockBigArrays(new MockPageCacheRecycler(Settings.EMPTY), new NoneCircuitBreakerService());
 
@@ -551,7 +561,7 @@ protected Engine.Searcher acquireSearcherInternal(String source) {
         }
     }
 
-    public void testSearchPathEvaluationUsingSortField() throws Exception {
+    public void testSearchPathEvaluation() throws Exception {
         ShardSearchRequest shardSearchRequest = mock(ShardSearchRequest.class);
         when(shardSearchRequest.searchType()).thenReturn(SearchType.DEFAULT);
         ShardId shardId = new ShardId("index", UUID.randomUUID().toString(), 1);
@@ -578,9 +588,24 @@ public void testSearchPathEvaluationUsingSortField() throws Exception {
         IndexMetadata indexMetadata = IndexMetadata.builder("index").settings(settings).build();
         IndexSettings indexSettings = new IndexSettings(indexMetadata, Settings.EMPTY);
         when(indexService.getIndexSettings()).thenReturn(indexSettings);
+        when(indexShard.indexSettings()).thenReturn(indexSettings);
 
         BigArrays bigArrays = new MockBigArrays(new MockPageCacheRecycler(Settings.EMPTY), new NoneCircuitBreakerService());
 
+        IndexShard systemIndexShard = mock(IndexShard.class);
+        when(systemIndexShard.getQueryCachingPolicy()).thenReturn(queryCachingPolicy);
+        when(systemIndexShard.getThreadPool()).thenReturn(threadPool);
+        when(systemIndexShard.isSystem()).thenReturn(true);
+
+        IndexShard throttledIndexShard = mock(IndexShard.class);
+        when(throttledIndexShard.getQueryCachingPolicy()).thenReturn(queryCachingPolicy);
+        when(throttledIndexShard.getThreadPool()).thenReturn(threadPool);
+        IndexSettings throttledIndexSettings = new IndexSettings(
+            indexMetadata,
+            Settings.builder().put(INDEX_SEARCH_THROTTLED.getKey(), true).build()
+        );
+        when(throttledIndexShard.indexSettings()).thenReturn(throttledIndexSettings);
+
         try (Directory dir = newDirectory(); RandomIndexWriter w = new RandomIndexWriter(random(), dir)) {
 
             final Supplier<Engine.SearcherSupplier> searcherSupplier = () -> new Engine.SearcherSupplier(Function.identity()) {
@@ -697,6 +722,62 @@ protected Engine.Searcher acquireSearcherInternal(String source) {
             }
             assertThrows(SetOnce.AlreadySetException.class, context::evaluateRequestShouldUseConcurrentSearch);
 
+            // Case 4: With a system index concurrent segment search is not used
+            readerContext = new ReaderContext(
+                newContextId(),
+                indexService,
+                systemIndexShard,
+                searcherSupplier.get(),
+                randomNonNegativeLong(),
+                false
+            );
+            context = new DefaultSearchContext(
+                readerContext,
+                shardSearchRequest,
+                target,
+                null,
+                bigArrays,
+                null,
+                null,
+                null,
+                false,
+                Version.CURRENT,
+                false,
+                executor,
+                null
+            );
+            context.evaluateRequestShouldUseConcurrentSearch();
+            assertFalse(context.shouldUseConcurrentSearch());
+            assertThrows(SetOnce.AlreadySetException.class, context::evaluateRequestShouldUseConcurrentSearch);
+
+            // Case 5: When search is throttled concurrent segment search is not used
+            readerContext = new ReaderContext(
+                newContextId(),
+                indexService,
+                throttledIndexShard,
+                searcherSupplier.get(),
+                randomNonNegativeLong(),
+                false
+            );
+            context = new DefaultSearchContext(
+                readerContext,
+                shardSearchRequest,
+                target,
+                null,
+                bigArrays,
+                null,
+                null,
+                null,
+                false,
+                Version.CURRENT,
+                false,
+                executor,
+                null
+            );
+            context.evaluateRequestShouldUseConcurrentSearch();
+            assertFalse(context.shouldUseConcurrentSearch());
+            assertThrows(SetOnce.AlreadySetException.class, context::evaluateRequestShouldUseConcurrentSearch);
+
             // shutdown the threadpool
             threadPool.shutdown();
         }