diff --git a/src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp b/src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp
index 8fc16b206f..1cc8e75494 100644
--- a/src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp
+++ b/src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp
@@ -262,6 +262,10 @@ void NeighborSearch<SortPolicy, MetricType, TreeType>::Search(
             oldFromNewReferences[(*neighborPtr)(j, i)];
       }
     }
+
+    // Finished with temporary matrices.
+    delete neighborPtr;
+    delete distancePtr;
   }
   else if (treeOwner && hasQuerySet && singleMode) // Map only references.
   {