diff --git a/src/Databases/DatabaseOrdinary.cpp b/src/Databases/DatabaseOrdinary.cpp
index 644bed23350..ef8b0eaae4f 100644
--- a/src/Databases/DatabaseOrdinary.cpp
+++ b/src/Databases/DatabaseOrdinary.cpp
@@ -46,12 +46,14 @@ static constexpr size_t METADATA_FILE_BUFFER_SIZE = 32768;
 DatabaseOrdinary::DatabaseOrdinary(const String & name_, const String & metadata_path_, ContextPtr context_)
     : DatabaseOrdinary(name_, metadata_path_, "data/" + escapeForFileName(name_) + "/", "DatabaseOrdinary (" + name_ + ")", context_)
 {
+    getContext()->addWarningMessageAboutDatabaseOrdinary(name_);
 }
 
 DatabaseOrdinary::DatabaseOrdinary(
     const String & name_, const String & metadata_path_, const String & data_path_, const String & logger, ContextPtr context_)
     : DatabaseOnDisk(name_, metadata_path_, data_path_, logger, context_)
 {
+    getContext()->addWarningMessageAboutDatabaseOrdinary(name_);
 }
 
 void DatabaseOrdinary::loadStoredObjects(ContextMutablePtr, LoadingStrictnessLevel)
diff --git a/src/Interpreters/Context.cpp b/src/Interpreters/Context.cpp
index 0e5897e7306..3c0cddf4a15 100644
--- a/src/Interpreters/Context.cpp
+++ b/src/Interpreters/Context.cpp
@@ -1171,6 +1171,30 @@ void Context::addWarningMessage(const String & msg) const
         shared->addWarningMessage(msg);
 }
 
+void Context::addWarningMessageAboutDatabaseOrdinary(const String & database_name) const
+{
+    std::lock_guard lock(shared->mutex);
+
+    /// We would like to report only about the first database with engine Ordinary
+    static std::atomic_bool is_called = false;
+    if (is_called.exchange(true))
+        return;
+
+    auto suppress_re = shared->getConfigRefWithLock(lock).getString("warning_supress_regexp", "");
+    /// We don't use getFlagsPath method, because it takes a shared lock.
+    auto convert_databases_flag = fs::path(shared->flags_path) / "convert_ordinary_to_atomic";
+    auto message = fmt::format("Server has databases (for example `{}`) with Ordinary engine, which was deprecated.\n"
+            "To convert this database to a new Atomic engine, please create a forcing flag {} and make sure that ClickHouse has write permission for it.\n"
+            "Example:\n"
+            "sudo touch '{}' && sudo chmod 666 '{}'",
+            database_name,
+            convert_databases_flag.string(), convert_databases_flag.string(), convert_databases_flag.string());
+
+    bool is_supressed = !suppress_re.empty() && re2::RE2::PartialMatch(message, suppress_re);
+    if (!is_supressed)
+        shared->addWarningMessage(message);
+}
+
 void Context::setConfig(const ConfigurationPtr & config)
 {
     shared->setConfig(config);
diff --git a/src/Interpreters/Context.h b/src/Interpreters/Context.h
index 8d40ccb301b..cac8c4c6ad3 100644
--- a/src/Interpreters/Context.h
+++ b/src/Interpreters/Context.h
@@ -532,6 +532,7 @@ public:
     void setUserScriptsPath(const String & path);
 
     void addWarningMessage(const String & msg) const;
+    void addWarningMessageAboutDatabaseOrdinary(const String & database_name) const;
 
     void setTemporaryStorageInCache(const String & cache_disk_name, size_t max_size);
     void setTemporaryStoragePolicy(const String & policy_name, size_t max_size);
diff --git a/src/Interpreters/loadMetadata.cpp b/src/Interpreters/loadMetadata.cpp
index 9543c70f49d..0b7a6dc92b0 100644
--- a/src/Interpreters/loadMetadata.cpp
+++ b/src/Interpreters/loadMetadata.cpp
@@ -227,26 +227,13 @@ LoadTaskPtrs loadMetadata(ContextMutablePtr context, const String & default_data
         databases.emplace(default_database_name, std::filesystem::path(path) / escapeForFileName(default_database_name));
     }
 
-    bool has_ordinary_databases = false;
     TablesLoader::Databases loaded_databases;
     for (const auto & [name, db_path] : databases)
     {
         loadDatabase(context, name, db_path, has_force_restore_data_flag);
-
-        auto database = DatabaseCatalog::instance().getDatabase(name);
-        loaded_databases.insert({name, database});
-        
-
-        if (database->getEngineName() == "Ordinary")
-            has_ordinary_databases = true;
-        
-        loaded_databases.insert({name,database});
+        loaded_databases.insert({name, DatabaseCatalog::instance().getDatabase(name)});
     }
 
-    if (has_ordinary_databases)
-        context->addWarningMessage("Server has databases with Ordinary engine, which is not optimal. \n " 
-        "To convert this database to a new Atomic engine, please create a flag named `convert_ordinary_to_atomic` in flags directory");
-    
     auto mode = getLoadingStrictnessLevel(/* attach */ true, /* force_attach */ true, has_force_restore_data_flag);
     TablesLoader loader{context, std::move(loaded_databases), mode};
     auto load_tasks = loader.loadTablesAsync();
diff --git a/tests/queries/0_stateless/02988_ordinary_database_warning.reference b/tests/queries/0_stateless/02988_ordinary_database_warning.reference
new file mode 100644
index 00000000000..587579af915
--- /dev/null
+++ b/tests/queries/0_stateless/02988_ordinary_database_warning.reference
@@ -0,0 +1 @@
+Ok.
diff --git a/tests/queries/0_stateless/02988_ordinary_database_warning.sql b/tests/queries/0_stateless/02988_ordinary_database_warning.sql
new file mode 100644
index 00000000000..cfa3eb42f53
--- /dev/null
+++ b/tests/queries/0_stateless/02988_ordinary_database_warning.sql
@@ -0,0 +1,8 @@
+DROP DATABASE IF EXISTS 02988_ordinary;
+
+SET allow_deprecated_database_ordinary = 1;
+CREATE DATABASE 02988_ordinary ENGINE=Ordinary;
+
+SELECT 'Ok.' FROM system.warnings WHERE message ILIKE '%Ordinary%' and message ILIKE '%deprecated%';
+
+DROP DATABASE IF EXISTS 02988_ordinary;