diff --git a/apps/emqx/test/emqx_persistent_messages_SUITE.erl b/apps/emqx/test/emqx_persistent_messages_SUITE.erl
index 530be9a4b..b2a41b0d2 100644
--- a/apps/emqx/test/emqx_persistent_messages_SUITE.erl
+++ b/apps/emqx/test/emqx_persistent_messages_SUITE.erl
@@ -41,6 +41,7 @@ end_per_suite(_Config) ->
 init_per_testcase(t_session_subscription_iterators = TestCase, Config) ->
     Cluster = cluster(),
     Nodes = emqx_cth_cluster:start(Cluster, #{work_dir => emqx_cth_suite:work_dir(TestCase, Config)}),
+    _ = wait_shards_online(Nodes),
     [{nodes, Nodes} | Config];
 init_per_testcase(t_message_gc = TestCase, Config) ->
     Opts = #{
@@ -53,7 +54,6 @@ init_per_testcase(TestCase, Config) ->
     common_init_per_testcase(TestCase, Config, _Opts = #{}).
 
 common_init_per_testcase(TestCase, Config, Opts) ->
-    ok = emqx_ds:drop_db(?PERSISTENT_MESSAGE_DB),
     Apps = emqx_cth_suite:start(
         app_specs(Opts),
         #{work_dir => emqx_cth_suite:work_dir(TestCase, Config)}
@@ -63,14 +63,11 @@ common_init_per_testcase(TestCase, Config, Opts) ->
 end_per_testcase(t_session_subscription_iterators, Config) ->
     Nodes = ?config(nodes, Config),
     emqx_common_test_helpers:call_janitor(60_000),
-    ok = emqx_cth_cluster:stop(Nodes),
-    end_per_testcase(common, Config);
+    ok = emqx_cth_cluster:stop(Nodes);
 end_per_testcase(_TestCase, Config) ->
     Apps = proplists:get_value(apps, Config, []),
     emqx_common_test_helpers:call_janitor(60_000),
-    clear_db(),
-    emqx_cth_suite:stop(Apps),
-    ok.
+    ok = emqx_cth_suite:stop(Apps).
 
 t_messages_persisted(_Config) ->
     C1 = connect(<<?MODULE_STRING "1">>, true, 30),
@@ -520,23 +517,24 @@ app_specs(Opts) ->
     ].
 
 cluster() ->
-    ExtraConf = "\n session_persistence.storage.builtin.n_sites = 2",
+    ExtraConf = "\n durable_storage.messages.n_sites = 2",
     Spec = #{role => core, apps => app_specs(#{extra_emqx_conf => ExtraConf})},
     [
         {persistent_messages_SUITE1, Spec},
         {persistent_messages_SUITE2, Spec}
     ].
 
+wait_shards_online(Nodes = [Node | _]) ->
+    NShards = erpc:call(Node, emqx_ds_replication_layer_meta, n_shards, [?PERSISTENT_MESSAGE_DB]),
+    ?retry(500, 10, [?assertEqual(NShards, shards_online(N)) || N <- Nodes]).
+
+shards_online(Node) ->
+    length(erpc:call(Node, emqx_ds_builtin_db_sup, which_shards, [?PERSISTENT_MESSAGE_DB])).
+
 get_mqtt_port(Node, Type) ->
     {_IP, Port} = erpc:call(Node, emqx_config, get, [[listeners, Type, default, bind]]),
     Port.
 
-clear_db() ->
-    ok = emqx_ds:drop_db(?PERSISTENT_MESSAGE_DB),
-    mria:stop(),
-    ok = mnesia:delete_schema([node()]),
-    ok.
-
 message(Topic, Payload, PublishedAt) ->
     #message{
         topic = Topic,
diff --git a/apps/emqx_durable_storage/src/emqx_ds_replication_layer_meta.erl b/apps/emqx_durable_storage/src/emqx_ds_replication_layer_meta.erl
index 726c81ff3..a4331cdea 100644
--- a/apps/emqx_durable_storage/src/emqx_ds_replication_layer_meta.erl
+++ b/apps/emqx_durable_storage/src/emqx_ds_replication_layer_meta.erl
@@ -276,6 +276,7 @@ allocate_shards_trans(DB, Opts) ->
     NShards = maps:get(n_shards, Opts),
     NSites = maps:get(n_sites, Opts),
     ReplicationFactor = maps:get(replication_factor, Opts),
+    NReplicas = min(NSites, ReplicationFactor),
     Shards = [integer_to_binary(I) || I <- lists:seq(0, NShards - 1)],
     AllSites = mnesia:match_object(?NODE_TAB, #?NODE_TAB{_ = '_'}, read),
     case length(AllSites) of
@@ -291,12 +292,18 @@ allocate_shards_trans(DB, Opts) ->
             ShardsAllocated = [Shard || #?SHARD_TAB{shard = {_DB, Shard}} <- Records],
             mnesia:abort({shards_already_allocated, ShardsAllocated})
     end,
+    {Allocation, _} = lists:mapfoldl(
+        fun(Shard, SSites) ->
+            {Sites, _} = emqx_utils_stream:consume(NReplicas, SSites),
+            {_, SRest} = emqx_utils_stream:consume(1, SSites),
+            {{Shard, Sites}, SRest}
+        end,
+        emqx_utils_stream:repeat(emqx_utils_stream:list(AllSites)),
+        Shards
+    ),
     lists:map(
-        fun(Shard) ->
-            Hashes0 = [{hash(Shard, Site), Site} || #?NODE_TAB{site = Site} <- AllSites],
-            Hashes = lists:sort(Hashes0),
-            {_, Sites} = lists:unzip(Hashes),
-            ReplicaSet = lists:sublist(Sites, 1, ReplicationFactor),
+        fun({Shard, Sites}) ->
+            ReplicaSet = [Site || #?NODE_TAB{site = Site} <- Sites],
             Record = #?SHARD_TAB{
                 shard = {DB, Shard},
                 replica_set = ReplicaSet
@@ -304,7 +311,7 @@ allocate_shards_trans(DB, Opts) ->
             ok = mnesia:write(Record),
             Shard
         end,
-        Shards
+        Allocation
     ).
 
 -spec update_db_config_trans(emqx_ds:db(), emqx_ds_replication_layer:builtin_db_opts()) ->
@@ -387,10 +394,6 @@ ensure_site() ->
     persistent_term:put(?emqx_ds_builtin_site, Site),
     ok.
 
--spec hash(emqx_ds_replication_layer:shard_id(), site()) -> any().
-hash(Shard, Site) ->
-    erlang:phash2({Shard, Site}).
-
 eval_qlc(Q) ->
     case mnesia:is_transaction() of
         true ->