diff --git a/src/Stache/Query/Builder.php b/src/Stache/Query/Builder.php
index 0f3a7fba9f3..58dfd01bade 100644
--- a/src/Stache/Query/Builder.php
+++ b/src/Stache/Query/Builder.php
@@ -143,7 +143,7 @@ protected function getCountForPagination()
 
     protected function getItems($keys)
     {
-        return $this->store->getItems($keys);
+        return $this->store->getItems($keys)->filter()->values();
     }
 
     protected function filterWhereBasic($values, $where)
diff --git a/tests/Stache/Repositories/EntryRepositoryTest.php b/tests/Stache/Repositories/EntryRepositoryTest.php
index 0bdb1cf80fa..e6fb299c134 100644
--- a/tests/Stache/Repositories/EntryRepositoryTest.php
+++ b/tests/Stache/Repositories/EntryRepositoryTest.php
@@ -71,6 +71,21 @@ public function it_gets_all_entries()
         ], $entries->map->id()->sort()->values()->all());
     }
 
+    #[Test]
+    public function it_ignores_keys_in_indexes_that_no_longer_have_corresponding_files()
+    {
+        $store = $this->stache->store('entries')->store('alphabetical');
+
+        $store->index('title')->load();
+        (function () {
+            $this->paths = $this->paths()->forget('alphabetical-bravo');
+        })->call($store);
+
+        $entries = $this->repo->query()->whereIn('title', ['Alpha', 'Bravo', 'Zulu'])->get();
+
+        $this->assertEquals(['alphabetical-alpha', 'alphabetical-zulu'], $entries->map->id()->all());
+    }
+
     #[Test]
     public function it_gets_entries_from_a_collection()
     {