diff --git a/src/client/opamSolution.ml b/src/client/opamSolution.ml
index b0adf8673ea..905d53cd82d 100644
--- a/src/client/opamSolution.ml
+++ b/src/client/opamSolution.ml
@@ -1189,8 +1189,10 @@ let install_sys_packages ~map_sysmap ~confirm env config sys_packages t =
     | `Ignore -> bypass t
     | `Quit -> give_up_msg (); OpamStd.Sys.exit_because `Aborted
   and print_command sys_packages =
+    (* Ensure that setup-x86_64.exe exists, so that an invalid command is not
+       displayed to the user. *)
     if OpamSysPoll.os_distribution env = Some "cygwin" then
-      OpamSysInteract.Cygwin.check_setup None;
+      OpamSysInteract.Cygwin.check_setup ~update:false;
     let commands =
       OpamSysInteract.install_packages_commands ~env config sys_packages
       |> List.map (fun ((`AsAdmin c | `AsUser c), a) -> c::a)
@@ -1222,7 +1224,7 @@ let install_sys_packages ~map_sysmap ~confirm env config sys_packages t =
   and auto_install t sys_packages =
     try
       if OpamSysPoll.os_distribution env = Some "cygwin" then
-        OpamSysInteract.Cygwin.check_setup None;
+        OpamSysInteract.Cygwin.check_setup ~update:true;
       OpamSysInteract.install ~env config sys_packages; (* handles dry_run *)
       map_sysmap (fun _ -> OpamSysPkg.Set.empty) t
     with Failure msg ->
diff --git a/src/state/opamSysInteract.ml b/src/state/opamSysInteract.ml
index dd0478e4f24..c14b8f1eb26 100644
--- a/src/state/opamSysInteract.ml
+++ b/src/state/opamSysInteract.ml
@@ -454,22 +454,9 @@ module Cygwin = struct
     | `Cygwin -> root / "bin"
 
   (* Set setup.exe in the good place, ie in .opam/.cygwin/ *)
-  let check_setup setup =
+  let check_setup ~update =
     let dst = cygsetup () in
-    match setup with
-    | Some setup ->
-      log "Copying %s into %s"
-          (OpamFilename.to_string setup)
-          (OpamFilename.to_string dst);
-      let sha512 =
-        OpamHash.compute ~kind:`SHA512 (OpamFilename.to_string setup)
-      in
-      OpamFilename.copy ~src:setup ~dst;
-      let checksum_file = OpamFilename.add_extension dst "sha512" in
-      OpamFilename.remove checksum_file;
-      OpamFilename.with_open_out_bin checksum_file @@ fun c ->
-        output_string c (OpamHash.contents sha512)
-    | None ->
+    if update || not (OpamFilename.exists dst) then
       OpamProcess.Job.run @@ download_setupexe dst
 end
 
@@ -1159,8 +1146,13 @@ let update ?(env=OpamVariable.Map.empty) config =
   in
   match cmd with
   | None ->
+    (* Cygwin doesn't have an update database per se, but one is supposed to use
+       the most current setup program when downloading setup.ini (which is the
+       package database (cf. the --no-version-check option).
+       Also, when #5839 is addressed, we'll need to cache setup.ini, and that
+       will want to be updated here too. *)
     if family = Cygwin then
-      Cygwin.check_setup None
+      Cygwin.check_setup ~update:true
     else
       OpamConsole.warning
         "Unknown update command for %s, skipping system update"
diff --git a/src/state/opamSysInteract.mli b/src/state/opamSysInteract.mli
index d9df5ba3b3b..9254c9a00f6 100644
--- a/src/state/opamSysInteract.mli
+++ b/src/state/opamSysInteract.mli
@@ -74,10 +74,11 @@ module Cygwin : sig
   (* Returns true if Cygwin install is internal *)
   val is_internal: OpamFile.Config.t -> bool
 
-  (* [check_setup path] checks and store Cygwin setup executable. Is [path] is
-     [None], it downloads it, otherwise it copies it to
-     <opamroot>/.cygwin/setup-x86_64.exe. *)
-  val check_setup: OpamFilename.t option -> unit
+  (* [check_setup ~update] downloads and stores a Cygwin setup executable to
+     <opamroot>/.cygwin/setup-x86_64.exe. If [~update = false], this only
+     happens if the setup executable does not already exist, otherwise it is.
+     updated. *)
+  val check_setup: update:bool -> unit
 
   (* Return Cygwin binary path *)
   val cygbin_opt: OpamFile.Config.t -> OpamFilename.Dir.t option