diff --git a/master_changes.md b/master_changes.md
index 5dad46f64cc..53af43ebbaf 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -133,6 +133,7 @@ users)
 # API updates
 ## 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]
 
 ## opam-repository
 
diff --git a/src/client/opamClient.ml b/src/client/opamClient.ml
index 85682f7dcb0..835e57f00c6 100644
--- a/src/client/opamClient.ml
+++ b/src/client/opamClient.ml
@@ -813,7 +813,24 @@ let windows_checks ?cygwin_setup ?git_location config =
           OpamStd.Sys.exit_because `Aborted
     in
     let config =
-      if is_msys2 cygcheck then config else
+      if is_msys2 cygcheck then
+        let env =
+          OpamStd.Env.cyg_env ~cygbin:(OpamFilename.Dir.to_string cygbin)
+            ~git_location:None
+        in
+        match OpamSystem.resolve_command ~env "pacman.exe" with
+        | Some pacman ->
+          if OpamConsole.confirm
+              "Found package manager pacman binary at %s.\n\
+               Do you want to use it for depexts?"
+              pacman then
+            OpamFile.Config.with_sys_pkg_manager_cmd
+              (OpamStd.String.Map.add distrib (OpamFilename.of_string pacman)
+                 (OpamFile.Config.sys_pkg_manager_cmd config))
+              config
+          else config
+        | None -> config
+      else
         OpamFile.Config.with_sys_pkg_manager_cmd
           (OpamStd.String.Map.add distrib cygcheck
              (OpamFile.Config.sys_pkg_manager_cmd config))