diff --git a/icing/file/version-util.cc b/icing/file/version-util.cc
index dd233e0..95af552 100644
--- a/icing/file/version-util.cc
+++ b/icing/file/version-util.cc
@@ -135,6 +135,10 @@
         // version 2 -> version 3 upgrade, no need to rebuild
         break;
       }
+      case 3: {
+        // version 3 -> version 4 upgrade, no need to rebuild
+        break;
+      }
       default:
         // This should not happen. Rebuild anyway if unsure.
         should_rebuild |= true;
diff --git a/icing/file/version-util.h b/icing/file/version-util.h
index b2d51df..553042f 100644
--- a/icing/file/version-util.h
+++ b/icing/file/version-util.h
@@ -32,13 +32,15 @@
 // - Version 2: M-2023-09, M-2023-11, M-2024-01. Schema is compatible with v1.
 //   (There were no M-2023-10, M-2023-12).
 // - Version 3: M-2024-02. Schema is compatible with v1 and v2.
+// - Version 4: M-2024-06. Schema is compatible with v1, v2 and v3.
 //
 // LINT.IfChange(kVersion)
-inline static constexpr int32_t kVersion = 3;
+inline static constexpr int32_t kVersion = 4;
 // LINT.ThenChange(//depot/google3/icing/schema/schema-store.cc:min_overlay_version_compatibility)
 inline static constexpr int32_t kVersionOne = 1;
 inline static constexpr int32_t kVersionTwo = 2;
 inline static constexpr int32_t kVersionThree = 3;
+inline static constexpr int32_t kVersionFour = 4;
 
 inline static constexpr int kVersionZeroFlashIndexMagic = 0x6dfba6ae;
 
diff --git a/icing/icing-search-engine.cc b/icing/icing-search-engine.cc
index 72be4e9..88e2998 100644
--- a/icing/icing-search-engine.cc
+++ b/icing/icing-search-engine.cc
@@ -231,8 +231,7 @@
 }
 
 bool IsV2QualifiedIdJoinIndexEnabled(const IcingSearchEngineOptions& options) {
-  return options.use_new_qualified_id_join_index() &&
-         options.document_store_namespace_id_fingerprint();
+  return true;
 }
 
 libtextclassifier3::StatusOr<std::unique_ptr<QualifiedIdJoinIndex>>
@@ -690,7 +689,7 @@
     // Discard index directory and instantiate a new one.
     Index::Options index_options(
         index_dir, options_.index_merge_size(),
-        options_.lite_index_sort_at_indexing(), options_.lite_index_sort_size(),
+        /*lite_index_sort_at_indexing=*/true, options_.lite_index_sort_size(),
         options_.build_property_existence_metadata_hits());
     if (!filesystem_->DeleteDirectoryRecursively(index_dir.c_str()) ||
         !filesystem_->CreateDirectoryRecursively(index_dir.c_str())) {
@@ -823,8 +822,8 @@
       DocumentStore::Create(
           filesystem_.get(), document_dir, clock_.get(), schema_store_.get(),
           force_recovery_and_revalidate_documents,
-          options_.document_store_namespace_id_fingerprint(),
-          options_.pre_mapping_fbv(), options_.use_persistent_hash_map(),
+          /*document_store_namespace_id_fingerprint=*/true,
+          /*pre_mapping_fbv=*/false, /*use_persistent_hash_map=*/true,
           options_.compression_level(), initialize_stats));
   document_store_ = std::move(create_result.document_store);
 
@@ -844,7 +843,7 @@
   }
   Index::Options index_options(
       index_dir, options_.index_merge_size(),
-      options_.lite_index_sort_at_indexing(), options_.lite_index_sort_size(),
+      /*lite_index_sort_at_indexing=*/true, options_.lite_index_sort_size(),
       options_.build_property_existence_metadata_hits());
 
   // Term index
@@ -2391,8 +2390,8 @@
     auto create_result_or = DocumentStore::Create(
         filesystem_.get(), current_document_dir, clock_.get(),
         schema_store_.get(), /*force_recovery_and_revalidate_documents=*/false,
-        options_.document_store_namespace_id_fingerprint(),
-        options_.pre_mapping_fbv(), options_.use_persistent_hash_map(),
+        /*document_store_namespace_id_fingerprint=*/true,
+        /*pre_mapping_fbv=*/false, /*use_persistent_hash_map=*/true,
         options_.compression_level(), /*initialize_stats=*/nullptr);
     // TODO(b/144458732): Implement a more robust version of
     // TC_ASSIGN_OR_RETURN that can support error logging.
@@ -2419,8 +2418,8 @@
   auto create_result_or = DocumentStore::Create(
       filesystem_.get(), current_document_dir, clock_.get(),
       schema_store_.get(), /*force_recovery_and_revalidate_documents=*/false,
-      options_.document_store_namespace_id_fingerprint(),
-      options_.pre_mapping_fbv(), options_.use_persistent_hash_map(),
+      /*document_store_namespace_id_fingerprint=*/true,
+      /*pre_mapping_fbv=*/false, /*use_persistent_hash_map=*/true,
       options_.compression_level(), /*initialize_stats=*/nullptr);
   if (!create_result_or.ok()) {
     // Unable to create DocumentStore from the new file. Mark as uninitialized
diff --git a/icing/icing-search-engine_initialization_test.cc b/icing/icing-search-engine_initialization_test.cc
index 122e4af..00b7e5b 100644
--- a/icing/icing-search-engine_initialization_test.cc
+++ b/icing/icing-search-engine_initialization_test.cc
@@ -1084,10 +1084,9 @@
         DocumentStore::Create(
             filesystem(), GetDocumentDir(), &fake_clock, schema_store.get(),
             /*force_recovery_and_revalidate_documents=*/false,
-            /*namespace_id_fingerprint=*/
-            icing_options.document_store_namespace_id_fingerprint(),
+            /*namespace_id_fingerprint=*/true,
             /*pre_mapping_fbv=*/false,
-            /*use_persistent_hash_map=*/false,
+            /*use_persistent_hash_map=*/true,
             PortableFileBackedProtoLog<
                 DocumentWrapper>::kDeflateCompressionLevel,
             /*initialize_stats=*/nullptr));
@@ -5403,169 +5402,6 @@
   }
 }
 
-// TODO(b/275121148): deprecate this test after rollout join index v2.
-class IcingSearchEngineInitializationSwitchJoinIndexTest
-    : public IcingSearchEngineInitializationTest,
-      public ::testing::WithParamInterface<bool> {};
-TEST_P(IcingSearchEngineInitializationSwitchJoinIndexTest, SwitchJoinIndex) {
-  bool use_join_index_v2 = GetParam();
-
-  SchemaProto schema =
-      SchemaBuilder()
-          .AddType(SchemaTypeConfigBuilder().SetType("Person").AddProperty(
-              PropertyConfigBuilder()
-                  .SetName("name")
-                  .SetDataTypeString(TERM_MATCH_PREFIX, TOKENIZER_PLAIN)
-                  .SetCardinality(CARDINALITY_REQUIRED)))
-          .AddType(SchemaTypeConfigBuilder()
-                       .SetType("Message")
-                       .AddProperty(PropertyConfigBuilder()
-                                        .SetName("body")
-                                        .SetDataTypeString(TERM_MATCH_PREFIX,
-                                                           TOKENIZER_PLAIN)
-                                        .SetCardinality(CARDINALITY_REQUIRED))
-                       .AddProperty(PropertyConfigBuilder()
-                                        .SetName("indexableInteger")
-                                        .SetDataTypeInt64(NUMERIC_MATCH_RANGE)
-                                        .SetCardinality(CARDINALITY_REQUIRED))
-                       .AddProperty(PropertyConfigBuilder()
-                                        .SetName("senderQualifiedId")
-                                        .SetDataTypeJoinableString(
-                                            JOINABLE_VALUE_TYPE_QUALIFIED_ID)
-                                        .SetCardinality(CARDINALITY_OPTIONAL)))
-          .Build();
-
-  DocumentProto person =
-      DocumentBuilder()
-          .SetKey("namespace", "person")
-          .SetSchema("Person")
-          .AddStringProperty("name", "person")
-          .SetCreationTimestampMs(kDefaultCreationTimestampMs)
-          .Build();
-  DocumentProto message =
-      DocumentBuilder()
-          .SetKey("namespace", "message/1")
-          .SetSchema("Message")
-          .AddStringProperty("body", kIpsumText)
-          .AddInt64Property("indexableInteger", 123)
-          .AddStringProperty("senderQualifiedId", "namespace#person")
-          .SetCreationTimestampMs(kDefaultCreationTimestampMs)
-          .Build();
-
-  // 1. Create an index with message 3 documents.
-  {
-    IcingSearchEngineOptions options = GetDefaultIcingOptions();
-    options.set_document_store_namespace_id_fingerprint(true);
-    options.set_use_new_qualified_id_join_index(use_join_index_v2);
-
-    TestIcingSearchEngine icing(options, std::make_unique<Filesystem>(),
-                                std::make_unique<IcingFilesystem>(),
-                                std::make_unique<FakeClock>(),
-                                GetTestJniCache());
-
-    ASSERT_THAT(icing.Initialize().status(), ProtoIsOk());
-    ASSERT_THAT(icing.SetSchema(schema).status(), ProtoIsOk());
-
-    EXPECT_THAT(icing.Put(person).status(), ProtoIsOk());
-    EXPECT_THAT(icing.Put(message).status(), ProtoIsOk());
-    message = DocumentBuilder(message).SetUri("message/2").Build();
-    EXPECT_THAT(icing.Put(message).status(), ProtoIsOk());
-    message = DocumentBuilder(message).SetUri("message/3").Build();
-    EXPECT_THAT(icing.Put(message).status(), ProtoIsOk());
-  }
-
-  // 2. Create the index again changing join index version. This should trigger
-  //    join index restoration.
-  {
-    // Mock filesystem to observe and check the behavior of all indices.
-    auto mock_filesystem = std::make_unique<MockFilesystem>();
-    EXPECT_CALL(*mock_filesystem, DeleteDirectoryRecursively(_))
-        .WillRepeatedly(DoDefault());
-    // Ensure term index directory should never be discarded.
-    EXPECT_CALL(*mock_filesystem,
-                DeleteDirectoryRecursively(EndsWith("/index_dir")))
-        .Times(0);
-    // Ensure integer index directory should never be discarded, and Clear()
-    // should never be called (i.e. storage sub directory
-    // "*/integer_index_dir/*" should never be discarded).
-    EXPECT_CALL(*mock_filesystem,
-                DeleteDirectoryRecursively(EndsWith("/integer_index_dir")))
-        .Times(0);
-    EXPECT_CALL(*mock_filesystem,
-                DeleteDirectoryRecursively(HasSubstr("/integer_index_dir/")))
-        .Times(0);
-    // Ensure qualified id join index directory should be discarded once, and
-    // Clear() should never be called (i.e. storage sub directory
-    // "*/qualified_id_join_index_dir/*" should never be discarded).
-    EXPECT_CALL(*mock_filesystem, DeleteDirectoryRecursively(
-                                      EndsWith("/qualified_id_join_index_dir")))
-        .Times(1);
-    EXPECT_CALL(
-        *mock_filesystem,
-        DeleteDirectoryRecursively(HasSubstr("/qualified_id_join_index_dir/")))
-        .Times(0);
-
-    IcingSearchEngineOptions options = GetDefaultIcingOptions();
-    options.set_document_store_namespace_id_fingerprint(true);
-    options.set_use_new_qualified_id_join_index(!use_join_index_v2);
-
-    TestIcingSearchEngine icing(options, std::move(mock_filesystem),
-                                std::make_unique<IcingFilesystem>(),
-                                std::make_unique<FakeClock>(),
-                                GetTestJniCache());
-    InitializeResultProto initialize_result = icing.Initialize();
-    ASSERT_THAT(initialize_result.status(), ProtoIsOk());
-    EXPECT_THAT(initialize_result.initialize_stats().index_restoration_cause(),
-                Eq(InitializeStatsProto::NONE));
-    EXPECT_THAT(
-        initialize_result.initialize_stats().integer_index_restoration_cause(),
-        Eq(InitializeStatsProto::NONE));
-    EXPECT_THAT(initialize_result.initialize_stats()
-                    .qualified_id_join_index_restoration_cause(),
-                Eq(InitializeStatsProto::INCONSISTENT_WITH_GROUND_TRUTH));
-
-    // Verify qualified id join index works normally: join a query for
-    // `name:person` with a child query for `body:consectetur` based on the
-    // child's `senderQualifiedId` field.
-    SearchSpecProto search_spec;
-    search_spec.set_term_match_type(TermMatchType::EXACT_ONLY);
-    search_spec.set_query("name:person");
-    JoinSpecProto* join_spec = search_spec.mutable_join_spec();
-    join_spec->set_parent_property_expression(
-        std::string(JoinProcessor::kQualifiedIdExpr));
-    join_spec->set_child_property_expression("senderQualifiedId");
-    join_spec->set_aggregation_scoring_strategy(
-        JoinSpecProto::AggregationScoringStrategy::COUNT);
-    JoinSpecProto::NestedSpecProto* nested_spec =
-        join_spec->mutable_nested_spec();
-    SearchSpecProto* nested_search_spec = nested_spec->mutable_search_spec();
-    nested_search_spec->set_term_match_type(TermMatchType::EXACT_ONLY);
-    nested_search_spec->set_query("body:consectetur");
-    *nested_spec->mutable_scoring_spec() = GetDefaultScoringSpec();
-    *nested_spec->mutable_result_spec() = ResultSpecProto::default_instance();
-
-    ResultSpecProto result_spec = ResultSpecProto::default_instance();
-    result_spec.set_max_joined_children_per_parent_to_return(
-        std::numeric_limits<int32_t>::max());
-
-    SearchResultProto results = icing.Search(
-        search_spec, ScoringSpecProto::default_instance(), result_spec);
-    ASSERT_THAT(results.results(), SizeIs(1));
-    EXPECT_THAT(results.results(0).document().uri(), Eq("person"));
-    EXPECT_THAT(results.results(0).joined_results(), SizeIs(3));
-    EXPECT_THAT(results.results(0).joined_results(0).document().uri(),
-                Eq("message/3"));
-    EXPECT_THAT(results.results(0).joined_results(1).document().uri(),
-                Eq("message/2"));
-    EXPECT_THAT(results.results(0).joined_results(2).document().uri(),
-                Eq("message/1"));
-  }
-}
-
-INSTANTIATE_TEST_SUITE_P(IcingSearchEngineInitializationSwitchJoinIndexTest,
-                         IcingSearchEngineInitializationSwitchJoinIndexTest,
-                         testing::Values(true, false));
-
 class IcingSearchEngineInitializationVersionChangeTest
     : public IcingSearchEngineInitializationTest,
       public ::testing::WithParamInterface<version_util::VersionInfo> {};
@@ -5659,10 +5495,9 @@
         DocumentStore::Create(
             filesystem(), GetDocumentDir(), &fake_clock, schema_store.get(),
             /*force_recovery_and_revalidate_documents=*/false,
-            /*namespace_id_fingerprint=*/
-            icing_options.document_store_namespace_id_fingerprint(),
+            /*namespace_id_fingerprint=*/true,
             /*pre_mapping_fbv=*/false,
-            /*use_persistent_hash_map=*/false,
+            /*use_persistent_hash_map=*/true,
             PortableFileBackedProtoLog<
                 DocumentWrapper>::kDeflateCompressionLevel,
             /*initialize_stats=*/nullptr));
diff --git a/icing/schema/schema-store.cc b/icing/schema/schema-store.cc
index e17e388..6830787 100644
--- a/icing/schema/schema-store.cc
+++ b/icing/schema/schema-store.cc
@@ -486,7 +486,7 @@
       ICING_RETURN_IF_ERROR(schema_file_->Write(std::move(base_schema_ptr)));
 
       // LINT.IfChange(min_overlay_version_compatibility)
-      // Although the current version is 3, the schema is compatible with
+      // Although the current version is 4, the schema is compatible with
       // version 1, so min_overlay_version_compatibility should be 1.
       int32_t min_overlay_version_compatibility = version_util::kVersionOne;
       // LINT.ThenChange(//depot/google3/icing/file/version-util.h:kVersion)