diff --git a/apps/emqx_conf/src/emqx_cluster_rpc.erl b/apps/emqx_conf/src/emqx_cluster_rpc.erl
index 8ad30dc74..21bf96806 100644
--- a/apps/emqx_conf/src/emqx_cluster_rpc.erl
+++ b/apps/emqx_conf/src/emqx_cluster_rpc.erl
@@ -17,7 +17,7 @@
 -behaviour(gen_server).
 
 %% API
--export([start_link/0, mnesia/1]).
+-export([start_link/0, create_tables/0]).
 
 %% Note: multicall functions are statically checked by
 %% `emqx_bapi_trans' and `emqx_bpapi_static_checks' modules. Don't
@@ -65,8 +65,6 @@
 
 -export_type([tnx_id/0, succeed_num/0]).
 
--boot_mnesia({mnesia, [boot]}).
-
 -include_lib("emqx/include/logger.hrl").
 -include_lib("snabbkaffe/include/snabbkaffe.hrl").
 -include("emqx_conf.hrl").
@@ -99,7 +97,8 @@
 %%%===================================================================
 %%% API
 %%%===================================================================
-mnesia(boot) ->
+
+create_tables() ->
     ok = mria:create_table(?CLUSTER_MFA, [
         {type, ordered_set},
         {rlog_shard, ?CLUSTER_RPC_SHARD},
@@ -113,7 +112,11 @@ mnesia(boot) ->
         {storage, disc_copies},
         {record_name, cluster_rpc_commit},
         {attributes, record_info(fields, cluster_rpc_commit)}
-    ]).
+    ]),
+    [
+        ?CLUSTER_MFA,
+        ?CLUSTER_COMMIT
+    ].
 
 start_link() ->
     start_link(node(), ?MODULE, get_retry_ms()).
diff --git a/apps/emqx_conf/src/emqx_conf.app.src b/apps/emqx_conf/src/emqx_conf.app.src
index 25a936a7a..7a9ddb9f7 100644
--- a/apps/emqx_conf/src/emqx_conf.app.src
+++ b/apps/emqx_conf/src/emqx_conf.app.src
@@ -3,7 +3,7 @@
     {vsn, "0.1.34"},
     {registered, []},
     {mod, {emqx_conf_app, []}},
-    {applications, [kernel, stdlib, emqx_ctl]},
+    {applications, [kernel, stdlib]},
     {env, []},
     {modules, []}
 ]}.
diff --git a/apps/emqx_conf/src/emqx_conf_app.erl b/apps/emqx_conf/src/emqx_conf_app.erl
index 74a7a8f2e..654a6bfe4 100644
--- a/apps/emqx_conf/src/emqx_conf_app.erl
+++ b/apps/emqx_conf/src/emqx_conf_app.erl
@@ -27,6 +27,7 @@
 -include("emqx_conf.hrl").
 
 start(_StartType, _StartArgs) ->
+    ok = mria:wait_for_tables(emqx_cluster_rpc:create_tables()),
     try
         ok = init_conf()
     catch
diff --git a/apps/emqx_retainer/test/emqx_retainer_SUITE.erl b/apps/emqx_retainer/test/emqx_retainer_SUITE.erl
index 71b1ef900..5dad85a9c 100644
--- a/apps/emqx_retainer/test/emqx_retainer_SUITE.erl
+++ b/apps/emqx_retainer/test/emqx_retainer_SUITE.erl
@@ -47,8 +47,6 @@ common_tests() ->
     emqx_common_test_helpers:all(?MODULE) -- [t_reindex].
 
 -define(BASE_CONF, <<
-    ""
-    "\n"
     "retainer {\n"
     "    enable = true\n"
     "    msg_clear_interval = 0s\n"
@@ -64,7 +62,6 @@ common_tests() ->
     "        max_retained_messages = 0\n"
     "     }\n"
     "}"
-    ""
 >>).
 
 %%--------------------------------------------------------------------
@@ -72,18 +69,14 @@ common_tests() ->
 %%--------------------------------------------------------------------
 
 init_per_suite(Config) ->
-    emqx_common_test_helpers:start_apps([emqx_conf]),
-    load_conf(),
-    emqx_limiter_sup:start_link(),
-    timer:sleep(200),
-    ok = application:ensure_started(?APP),
-    Config.
+    Apps = emqx_cth_suite:start(
+        [emqx, emqx_conf, app_spec()],
+        #{work_dir => emqx_cth_suite:work_dir(Config)}
+    ),
+    [{suite_apps, Apps} | Config].
 
-end_per_suite(_Config) ->
-    ekka:stop(),
-    mria:stop(),
-    mria_mnesia:delete_schema(),
-    emqx_common_test_helpers:stop_apps([?APP, emqx_conf]).
+end_per_suite(Config) ->
+    emqx_cth_suite:stop(?config(suite_apps, Config)).
 
 init_per_group(mnesia_without_indices, Config) ->
     mnesia:clear_table(?TAB_INDEX_META),
@@ -113,10 +106,8 @@ init_per_testcase(t_get_basic_usage_info, Config) ->
 init_per_testcase(_TestCase, Config) ->
     Config.
 
-load_conf() ->
-    ok = emqx_config:delete_override_conf_files(),
-    emqx_ratelimiter_SUITE:init_config(),
-    ok = emqx_config:init_load(emqx_retainer_schema, ?BASE_CONF).
+app_spec() ->
+    {emqx_retainer, ?BASE_CONF}.
 
 %%--------------------------------------------------------------------
 %% Test Cases
diff --git a/apps/emqx_retainer/test/emqx_retainer_cli_SUITE.erl b/apps/emqx_retainer/test/emqx_retainer_cli_SUITE.erl
index c04f7a6de..335d10d4f 100644
--- a/apps/emqx_retainer/test/emqx_retainer_cli_SUITE.erl
+++ b/apps/emqx_retainer/test/emqx_retainer_cli_SUITE.erl
@@ -22,18 +22,20 @@
 -include("emqx_retainer.hrl").
 
 -include_lib("eunit/include/eunit.hrl").
+-include_lib("common_test/include/ct.hrl").
 -include_lib("snabbkaffe/include/snabbkaffe.hrl").
 
 all() -> emqx_common_test_helpers:all(?MODULE).
 
 init_per_suite(Config) ->
-    emqx_retainer_SUITE:load_conf(),
-    %% Start Apps
-    emqx_common_test_helpers:start_apps([emqx_retainer]),
-    Config.
+    Apps = emqx_cth_suite:start(
+        [emqx, emqx_conf, emqx_retainer_SUITE:app_spec()],
+        #{work_dir => emqx_cth_suite:work_dir(Config)}
+    ),
+    [{suite_apps, Apps} | Config].
 
-end_per_suite(_Config) ->
-    emqx_common_test_helpers:stop_apps([emqx_retainer]).
+end_per_suite(Config) ->
+    emqx_cth_suite:stop(?config(suite_apps, Config)).
 
 t_reindex_status(_Config) ->
     ok = emqx_retainer_mnesia_cli:retainer(["reindex", "status"]).
diff --git a/apps/emqx_retainer/test/emqx_retainer_mqtt_v5_SUITE.erl b/apps/emqx_retainer/test/emqx_retainer_mqtt_v5_SUITE.erl
index bfe5b6a00..9c24f587b 100644
--- a/apps/emqx_retainer/test/emqx_retainer_mqtt_v5_SUITE.erl
+++ b/apps/emqx_retainer/test/emqx_retainer_mqtt_v5_SUITE.erl
@@ -20,17 +20,19 @@
 -compile(nowarn_export_all).
 
 -include_lib("eunit/include/eunit.hrl").
+-include_lib("common_test/include/ct.hrl").
 
 all() -> emqx_common_test_helpers:all(?MODULE).
 
 init_per_suite(Config) ->
-    emqx_retainer_SUITE:load_conf(),
-    %% Start Apps
-    emqx_common_test_helpers:start_apps([emqx_retainer]),
-    Config.
+    Apps = emqx_cth_suite:start(
+        [emqx, emqx_conf, emqx_retainer_SUITE:app_spec()],
+        #{work_dir => emqx_cth_suite:work_dir(Config)}
+    ),
+    [{suite_apps, Apps} | Config].
 
-end_per_suite(_Config) ->
-    emqx_common_test_helpers:stop_apps([emqx_retainer]).
+end_per_suite(Config) ->
+    emqx_cth_suite:stop(?config(suite_apps, Config)).
 
 client_info(Key, Client) ->
     maps:get(Key, maps:from_list(emqtt:info(Client)), undefined).