diff --git a/src/Databases/DatabaseReplicated.cpp b/src/Databases/DatabaseReplicated.cpp
index 1f2d21d7f6a..1c13b0e8fcb 100644
--- a/src/Databases/DatabaseReplicated.cpp
+++ b/src/Databases/DatabaseReplicated.cpp
@@ -1206,6 +1206,13 @@ void DatabaseReplicated::recoverLostReplica(const ZooKeeperPtr & current_zookeep
         query_context->setSetting("database_replicated_allow_explicit_uuid", 3);
         query_context->setSetting("database_replicated_allow_replicated_engine_arguments", 3);
 
+        /// We apply the flatten_nested setting after writing the CREATE query to the DDL log,
+        /// but before writing metadata to ZooKeeper. So we have to apply the setting on secondary replicas, but not in recovery mode.
+        /// Set it to false, so it will do nothing on recovery. The metadata in ZooKeeper should be used as is.
+        /// Same for data_type_default_nullable.
+        query_context->setSetting("flatten_nested", false);
+        query_context->setSetting("data_type_default_nullable", false);
+
         auto txn = std::make_shared<ZooKeeperMetadataTransaction>(current_zookeeper, zookeeper_path, false, "");
         query_context->initZooKeeperMetadataTransaction(txn);
         return query_context;
diff --git a/tests/integration/test_replicated_database/test.py b/tests/integration/test_replicated_database/test.py
index 533eb601ad6..dd06665b648 100644
--- a/tests/integration/test_replicated_database/test.py
+++ b/tests/integration/test_replicated_database/test.py
@@ -103,11 +103,27 @@ def test_flatten_nested(started_cluster):
         "CREATE MATERIALIZED VIEW create_replicated_table.mv ENGINE=ReplicatedMergeTree ORDER BY tuple() AS select d, cast([(k, toString(i32))] as Nested(a UInt64, b String)) from create_replicated_table.replicated_table"
     )
 
-    assert main_node.query(
-        "show create create_replicated_table.mv"
-    ) == dummy_node.query("show create create_replicated_table.mv")
+    main_node.query(
+        "CREATE TABLE create_replicated_table.no_flatten (n Nested(a UInt64, b String)) ENGINE=ReplicatedMergeTree ORDER BY tuple();",
+        settings={"flatten_nested": 0},
+    )
+
+    snapshot_recovering_node.query(
+        "CREATE DATABASE create_replicated_table ENGINE = Replicated('/test/create_replicated_table', 'shard1', 'replica3');"
+    )
+    snapshot_recovering_node.query(
+        "SYSTEM SYNC DATABASE REPLICA create_replicated_table"
+    )
+
+    for node in [dummy_node, snapshot_recovering_node]:
+        for table in ["replicated_table", "mv", "no_flatten"]:
+            assert main_node.query(
+                f"show create create_replicated_table.{table}"
+            ) == node.query(f"show create create_replicated_table.{table}")
+
     main_node.query("DROP DATABASE create_replicated_table SYNC")
     dummy_node.query("DROP DATABASE create_replicated_table SYNC")
+    snapshot_recovering_node.query("DROP DATABASE create_replicated_table SYNC")
 
 
 def test_create_replicated_table(started_cluster):