diff --git a/src/client/opamClient.ml b/src/client/opamClient.ml
index 12f2345dbef..daf36d04388 100644
--- a/src/client/opamClient.ml
+++ b/src/client/opamClient.ml
@@ -1000,14 +1000,14 @@ let cygwin_searches ?first () =
   in
   seq cygwin_searches
 
-let rec cygwin_menu header =
+let rec cygwin_menu ~bypass_checks header =
   let string_of_kind = function
     | `Msys2 -> "MSYS2"
     | `Cygwin -> "Cygwin"
   in
   let start = Unix.gettimeofday () in
   let test_mechanism (roots, count, mechanisms) search =
-    match test_mechanism header search with
+    match test_mechanism ~bypass_checks header search with
     | Some ((kind, `Root root) as mechanism) ->
       if OpamFilename.Dir.Set.mem root roots then
         roots, count, mechanisms
@@ -1068,6 +1068,9 @@ let rec cygwin_menu header =
           "Use tools found in PATH (%s installation at %s)"
           (string_of_kind kind) root)::options
       in
+      if bypass_checks then
+        options, path_option, None
+      else
       (* Check whether cygcheck is still available in the initial environment.
          This allows a warning to be displayed reminding the user to continue
          running opam from a Cygwin/MSYS2 shell that has been manually started,
@@ -1167,11 +1170,11 @@ let rec cygwin_menu header =
           Some (kind, `Root root)
         | Error msg ->
           OpamConsole.error "%s" msg;
-          cygwin_menu header
+          cygwin_menu ~bypass_checks header
     end
   | `Abort -> OpamStd.Sys.exit_because `Aborted
 
-and test_mechanism header = function
+and test_mechanism ~bypass_checks header = function
   | (`Internal _) as mechanism -> Some (`Cygwin, mechanism)
   | `Path ->
      let cygcheck =
@@ -1195,7 +1198,7 @@ and test_mechanism header = function
     | Error msg ->
         OpamConsole.error_and_exit `Not_found "%s" msg
     end
-  | `Menu -> cygwin_menu header
+  | `Menu -> cygwin_menu ~bypass_checks header
 
 let string_of_cygwin_setup = function
   | `internal pkgs ->
@@ -1257,7 +1260,8 @@ let initialise_msys2 root =
       | `Quit ->
         OpamStd.Sys.exit_because `Aborted
 
-let determine_windows_configuration ?cygwin_setup ?git_location config =
+let determine_windows_configuration ?cygwin_setup ?git_location
+                                    ~bypass_checks config =
   OpamStd.Option.iter
     (log "Cygwin (from CLI): %a" (slog string_of_cygwin_setup)) cygwin_setup;
   (* Check whether symlinks can be created. Developer Mode is not the only way
@@ -1389,7 +1393,8 @@ let determine_windows_configuration ?cygwin_setup ?git_location config =
   (* Reduce mechanisms to a single mechanism (which may therefore display a
      menu). *)
   let kind, mechanism =
-    match OpamCompat.Seq.find_map (test_mechanism header) mechanisms with
+    let test_mechanism = test_mechanism ~bypass_checks header in
+    match OpamCompat.Seq.find_map test_mechanism mechanisms with
     | Some result -> result
     | None ->
       Lazy.force header;
@@ -1586,7 +1591,8 @@ let reinit ?(init_config=OpamInitDefaults.init_config()) ~interactive
   let config = update_with_init_config config init_config in
   let config, mechanism, system_packages, msys2_check_root =
     if Sys.win32 then
-      determine_windows_configuration ?cygwin_setup ?git_location config
+      determine_windows_configuration ?cygwin_setup ?git_location
+                                      ~bypass_checks config
     else
       config, None, [], None
   in
@@ -1673,7 +1679,8 @@ let init
         in
         let config, mechanism, system_packages, msys2_check_root =
           if Sys.win32 then
-            determine_windows_configuration ?cygwin_setup ?git_location config
+            determine_windows_configuration ?cygwin_setup ?git_location
+                                            ~bypass_checks config
           else
             config, None, [], None
         in