diff --git a/master_changes.md b/master_changes.md
index 53af43ebbaf..faede2280ab 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -134,6 +134,7 @@ users)
 ## opam-client
   * `OpamClient.windows_checks`: On existing cygwin install, permit to detect msys2 and store `os-distribution=msys2` in `global-variables` config file field [#5843 @rjbou]
   * `OpamClient.windows_checks`: When updating config file for msys2, resolve `pacman` path and store it in `sys-pkg-manager-cmd` for msys2 [#5843 @rjbou]
+  * `OpamArg.apply_global_options`: load MSYS2 Cygwin binary path too [#5843 @rjbou]
 
 ## opam-repository
 
@@ -141,6 +142,7 @@ users)
   * `OpamEnv.env_expansion`: Fix detection of out-of-date environment variables, a filter predicate was inverted [#5837 @dra27]
   * `OpamSysInteract.Cygwin.check_install`: add `variant` argument to permit checking that it is an Cygwin-like install if it is set to true, keep checking that it is a strictly Cygwin install if false [#5843 @rjbou]
   * `OpamSysInteract.Cygwin.check_install`: look for `cygcheck.exe` in `usr/bin` also as MSYS2 doesn't have "bin" [#5843 @rjbou]
+  * `OpamGlobalState.load_config`: load MSYS2 Cygwin binary path too at config file loading [#5843 @rjbou]
 
 ## opam-solver
 
diff --git a/src/client/opamArg.ml b/src/client/opamArg.ml
index b37db85f2cc..c43ff1f6382 100644
--- a/src/client/opamArg.ml
+++ b/src/client/opamArg.ml
@@ -600,6 +600,21 @@ let apply_global_options cli o =
             | _, element::elements -> aux (Some element) elements
           in
           aux None elements
+        | { pelem = Variable ({ pelem = "global-variables"; _},
+                              {pelem = List { pelem = elements; _}; _}); _} ->
+          let rec aux last elements =
+            match last, elements with
+            | _, [] -> ()
+            | Some { pelem = Ident "os-distribution"; _},
+              { pelem = String "msys2"; _}::_  ->
+              let cygbin =
+                OpamStd.Option.map Filename.dirname
+                  (OpamSystem.resolve_command "cygcheck")
+              in
+              OpamCoreConfig.update ?cygbin ()
+            | _, element::elements -> aux (Some element) elements
+          in
+          aux None elements
         | { pelem = Variable ({ pelem = "git-location"; _},
                               {pelem = String git_location; _}); _} ->
           OpamCoreConfig.update ~git_location ()
diff --git a/src/state/opamGlobalState.ml b/src/state/opamGlobalState.ml
index 811d20da2e1..b8140765dea 100644
--- a/src/state/opamGlobalState.ml
+++ b/src/state/opamGlobalState.ml
@@ -38,10 +38,22 @@ let load_config lock_kind global_lock root =
   let config =
     OpamFormatUpgrade.as_necessary lock_kind global_lock root config
   in
-  OpamStd.Option.iter
-    (fun cygbin ->
-       OpamCoreConfig.update ~cygbin:(OpamFilename.Dir.to_string cygbin) ())
-    (OpamSysInteract.Cygwin.cygbin_opt (fst config));
+  (* Update Cygwin variants cygbin *)
+  let cygbin =
+    let config = fst config in
+    match OpamSysInteract.Cygwin.cygbin_opt config with
+    | Some cygbin -> Some (OpamFilename.Dir.to_string cygbin)
+    | None ->
+      if List.exists (function
+          | (v, S "msys2", _) ->
+            String.equal (OpamVariable.to_string v) "os-distribution"
+          | _ -> false) (OpamFile.Config.global_variables config)
+      then
+        OpamStd.Option.map Filename.dirname
+          (OpamSystem.resolve_command "cygcheck")
+      else None
+  in
+  OpamCoreConfig.update ?cygbin ();
   config
 
 let inferred_from_system = "Inferred from system"