diff --git a/CHANGES b/CHANGES
index 03ea68f0c87..fa732979a06 100644
--- a/CHANGES
+++ b/CHANGES
@@ -6,7 +6,7 @@ are not marked). Those prefixed with "(+)" are new command/option (since
 2.1.0:
 * Set DEBIAN_FRONTEND=noninteractive for unsafe-yes confirmation level
   [#4735 @dra27 - partially fix #4731]
-* Fix 2.1~alpha2 to 2.1 format upgrade with reinit [#4750 @rjbou - fix #4748]
+* Fix 2.1~alpha2 to 2.1 format upgrade with reinit [#4750 #4756 @rjbou - fix #4748]
 * Fix bypass-check handling on reinit [#4750 @rjbou]
 * fish: fix deprecated redirection syntax `^` [#4736 @vzaliva]
 * Bump src_exts and fix build compat with Dune 2.9.0 [#4754 @dra27]
diff --git a/src/client/opamCliMain.ml b/src/client/opamCliMain.ml
index 9eb1218ef32..6d95049bae1 100644
--- a/src/client/opamCliMain.ml
+++ b/src/client/opamCliMain.ml
@@ -340,14 +340,20 @@ let rec main_catch_all f =
          Windows anyway. *)
     else
       Unix.execvpe cmd args env
-  | OpamFormatUpgrade.Upgrade_done conf ->
+  | OpamFormatUpgrade.Upgrade_done (conf, reinit) ->
     main_catch_all @@ fun () ->
     OpamConsole.header_msg "Rerunning init and update";
-    OpamClient.reinit ~interactive:true ~update_config:false ~bypass_checks:true
-      conf (OpamStd.Sys.guess_shell_compat ());
-    OpamConsole.msg
-      "Update done, please now retry your command.\n";
-    exit (OpamStd.Sys.get_exit_code `Aborted)
+    (match reinit with
+     | Some reinit ->
+       reinit conf;
+       OpamConsole.msg "Update done.\n";
+       exit (OpamStd.Sys.get_exit_code `Success)
+     | None ->
+       OpamClient.reinit ~interactive:true ~update_config:false
+         ~bypass_checks:true conf (OpamStd.Sys.guess_shell_compat ());
+       OpamConsole.msg
+         "Update done, please now retry your command.\n";
+       exit (OpamStd.Sys.get_exit_code `Aborted))
   | e ->
     flush stdout;
     flush stderr;
diff --git a/src/client/opamCommands.ml b/src/client/opamCommands.ml
index 5a03828526e..7ebfd1aab45 100644
--- a/src/client/opamCommands.ml
+++ b/src/client/opamCommands.ml
@@ -371,21 +371,26 @@ let init cli =
           get_init_config ~no_sandboxing
             ~no_default_config_file:no_config_file ~add_config_file:config_file
         in
+        let reinit conf =
+          OpamClient.reinit ~init_config ~interactive ~dot_profile
+            ?update_config ?env_hook ?completion ~inplace ~bypass_checks
+            ~check_sandbox:(not no_sandboxing)
+            conf shell
+        in
         let config =
           match OpamStateConfig.load ~lock_kind:`Lock_write root with
           | Some c -> c
           | exception (OpamPp.Bad_version _ as e) ->
-            OpamFormatUpgrade.hard_upgrade_from_2_1_intermediates root;
+            OpamFormatUpgrade.hard_upgrade_from_2_1_intermediates ~reinit root;
             raise e
           | None -> OpamFile.Config.empty
         in
-        OpamClient.reinit ~init_config ~interactive ~dot_profile
-          ?update_config ?env_hook ?completion ~inplace ~bypass_checks
-          ~check_sandbox:(not no_sandboxing)
-          config shell
+        reinit config
       else
-        (if not interactive &&
-            update_config <> Some true && completion <> Some true && env_hook <> Some true then
+        (if not interactive
+            && update_config <> Some true
+            && completion <> Some true
+            && env_hook <> Some true then
            OpamConsole.msg
              "Opam was already initialised. If you want to set it up again, \
               use `--interactive', `--reinit', or choose a different \
diff --git a/src/state/opamFormatUpgrade.ml b/src/state/opamFormatUpgrade.ml
index 23409e2c212..dc0afa10b5f 100644
--- a/src/state/opamFormatUpgrade.ml
+++ b/src/state/opamFormatUpgrade.ml
@@ -17,7 +17,7 @@ open OpamFilename.Op
 let log fmt = OpamConsole.log "FMT_UPG" fmt
 let slog = OpamConsole.slog
 
-exception Upgrade_done of OpamFile.Config.t
+exception Upgrade_done of OpamFile.Config.t * (OpamFile.Config.t -> unit) option
 
 (* - Package and aux functions - *)
 
@@ -1094,7 +1094,7 @@ let remove_missing_switches root conf =
   in
   OpamFile.Config.with_installed_switches exists conf, missing
 
-let as_necessary requested_lock global_lock root config =
+let as_necessary ?reinit requested_lock global_lock root config =
   let root_version =
     match OpamFile.Config.opam_root_version_opt config with
     | Some v -> v
@@ -1237,7 +1237,7 @@ let as_necessary requested_lock global_lock root config =
           let config = hard config |> light in
           OpamConsole.msg "Format upgrade done.\n";
           (* We need to re run init in case of hard upgrade *)
-          raise (Upgrade_done config)
+          raise (Upgrade_done (config, reinit))
         else
           OpamStd.Sys.exit_because `Aborted
       else
@@ -1255,7 +1255,7 @@ let as_necessary requested_lock global_lock root config =
     OpamConsole.error_and_exit `Locked
       "Could not acquire lock for performing format upgrade."
 
-let hard_upgrade_from_2_1_intermediates ?global_lock root =
+let hard_upgrade_from_2_1_intermediates ?reinit ?global_lock root =
   let config_f = OpamPath.config root in
   let opam_root_version = OpamFile.Config.raw_root_version config_f in
   match opam_root_version with
@@ -1290,7 +1290,7 @@ let hard_upgrade_from_2_1_intermediates ?global_lock root =
       | None -> OpamFilename.flock `Lock_read (OpamPath.lock root)
     in
     (* it will trigger only hard upgrades that won't get back *)
-    ignore @@ as_necessary `Lock_write global_lock root
+    ignore @@ as_necessary `Lock_write global_lock root ?reinit
       (OpamFile.Config.with_opam_root_version v2_1_alpha2 config)
 
 let opam_file ?(quiet=false) ?filename opam =
diff --git a/src/state/opamFormatUpgrade.mli b/src/state/opamFormatUpgrade.mli
index 377fc367a8b..48f89f48f16 100644
--- a/src/state/opamFormatUpgrade.mli
+++ b/src/state/opamFormatUpgrade.mli
@@ -16,8 +16,10 @@ open OpamTypes
 open OpamStateTypes
 
 (** Raised when the opam root has been updated to a newer format, and further
-    action (opam init/update) is needed. *)
-exception Upgrade_done of OpamFile.Config.t
+    action (opam init/update) is needed.
+    [Upgrade_done conf reinit] specifies the new config file and a reinit
+    function to call instead of default (see [OpamCliMain.main_catch_all]). *)
+exception Upgrade_done of OpamFile.Config.t * (OpamFile.Config.t -> unit) option
 
 (** The latest version of the opam root format, that normal operation of this
     instance of opam requires *)
@@ -32,7 +34,8 @@ val latest_version: OpamVersion.t
     when it's done raises [Upgrade_done updated_config]. Otherwise, it returns
     the upgraded or unchanged config file.*)
 val as_necessary:
-  'a lock -> OpamSystem.lock -> dirname -> OpamFile.Config.t -> OpamFile.Config.t
+  ?reinit:(OpamFile.Config.t -> unit) -> 'a lock -> OpamSystem.lock -> dirname ->
+  OpamFile.Config.t -> OpamFile.Config.t
 
 (* Try to launch a hard upgrade from 2;1 alpha's & beta's root
    to 2.1~rc one. Raises [Upgrade_done] (catched by main
@@ -40,7 +43,8 @@ val as_necessary:
    It is intend to be called after a config file that error with
    [OpamPp.Bad_version] *)
 val hard_upgrade_from_2_1_intermediates:
-  ?global_lock: OpamSystem.lock -> dirname -> unit
+  ?reinit:(OpamFile.Config.t -> unit) -> ?global_lock: OpamSystem.lock ->
+  dirname -> unit
 
 (** Converts the opam file format, including rewriting availability conditions
     based on OCaml-related variables into dependencies. The filename is used to
diff --git a/tests/reftests/opamroot-versions.test b/tests/reftests/opamroot-versions.test
index 4ad59ad9e71..a8264818e85 100644
--- a/tests/reftests/opamroot-versions.test
+++ b/tests/reftests/opamroot-versions.test
@@ -1628,8 +1628,7 @@ RSTATE                          Cache found
 
 <><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
 [default] no changes from file://${BASEDIR}/default
-Update done, please now retry your command.
-# Return code 10 #
+Update done.
 ### opam switch --short
 GSTATE                          LOAD-GLOBAL-STATE @ ${BASEDIR}/OPAM
 ${BASEDIR}