diff --git a/examples/client_batch.ml b/examples/client_batch.ml
index 8f647be66e..8889797ab0 100644
--- a/examples/client_batch.ml
+++ b/examples/client_batch.ml
@@ -18,11 +18,12 @@ module Store = Irmin_mem.KV.Make (Irmin.Contents.String)
 module Client = Irmin_client_unix.Make (Store)
 module Error = Irmin_client.Error
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   let info () = Client.Info.empty in
   let uri = Uri.of_string Sys.argv.(1) in
-  let client = Client.connect ~sw uri in
+  let client = Client.connect ~sw ~fs uri in
 
   let main = Client.main client in
   Client.set_exn ~info main [ "testing" ] "testing";
@@ -45,4 +46,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/custom_graphql.ml b/examples/custom_graphql.ml
index 5bd484d5bd..9a867f733b 100644
--- a/examples/custom_graphql.ml
+++ b/examples/custom_graphql.ml
@@ -106,11 +106,12 @@ end
 module Server =
   Irmin_graphql_unix.Server.Make_ext (Store) (Remote) (Custom_types)
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
   let config = Irmin_git.config Config.root in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let server = Server.v repo in
   let src = "localhost" in
   let port = 9876 in
@@ -123,4 +124,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/custom_merge.ml b/examples/custom_merge.ml
index 05296d1e54..036c25d3de 100644
--- a/examples/custom_merge.ml
+++ b/examples/custom_merge.ml
@@ -137,10 +137,11 @@ let print_logs name t =
   let logs = all_logs t in
   Fmt.pr "-----------\n%s:\n-----------\n%a%!" name (Irmin.Type.pp Log.t) logs
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.main repo in
 
   (* populate the log with some random messages *)
@@ -162,4 +163,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/custom_storage.ml b/examples/custom_storage.ml
index 245c17368f..72ffd87cfd 100644
--- a/examples/custom_storage.ml
+++ b/examples/custom_storage.ml
@@ -48,7 +48,7 @@ functor
 
     (** Initialisation / Closing *)
 
-    let v ~sw:_ config =
+    let v ~sw:_ ~fs:_ config =
       let init_size = Irmin.Backend.Conf.get config Hashtbl_config.init_size in
       { t = Tbl.create init_size; l = Eio.Mutex.create () }
 
@@ -86,9 +86,10 @@ module Store =
 let config ?(config = Hashtbl_config.empty) ?(init_size = 42) () =
   Irmin.Backend.Conf.add config Hashtbl_config.init_size init_size
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
-  let repo = Store.Repo.v ~sw (config ()) in
+  let fs = Eio.Stdenv.fs env in
+  let repo = Store.Repo.v ~sw ~fs (config ()) in
   let main = Store.main repo in
   let info () = Store.Info.v 0L in
   let key = "Hello" in
@@ -98,4 +99,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/deploy.ml b/examples/deploy.ml
index 4341a290c9..dec63addd2 100644
--- a/examples/deploy.ml
+++ b/examples/deploy.ml
@@ -80,7 +80,7 @@ let revert repo =
     Eio_unix.sleep 2.;
     Store.Head.set prod h2)
 
-let main () =
+let main env =
   let cmd = Sys.argv.(0) in
   let help () =
     Printf.eprintf
@@ -102,18 +102,19 @@ let main () =
       cmd cmd cmd cmd Config.root
   in
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   if Array.length Sys.argv <> 2 then help ()
   else
     match Sys.argv.(1) with
     | "provision" ->
-        (let repo = Store.Repo.v ~sw config in
+        (let repo = Store.Repo.v ~sw ~fs config in
          provision repo);
         Printf.printf
           "The VM is now provisioned. Run `%s configure` to simulate a sysadmin \n\
            configuration.\n"
           cmd
     | "configure" ->
-        (let repo = Store.Repo.v ~sw config in
+        (let repo = Store.Repo.v ~sw ~fs config in
          configure repo);
         Printf.printf
           "The VM is now configured. Run `%s attack` to simulate an attack by \
@@ -121,17 +122,17 @@ let main () =
            intruder.\n"
           cmd
     | "attack" ->
-        (let repo = Store.Repo.v ~sw config in
+        (let repo = Store.Repo.v ~sw ~fs config in
          attack repo);
         Printf.printf
           "The VM has been attacked. Run `%s revert` to revert the VM state to \
            a safe one.\n"
           cmd
     | "revert" ->
-        let repo = Store.Repo.v ~sw config in
+        let repo = Store.Repo.v ~sw ~fs config in
         revert repo
     | _ -> help ()
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/fold.ml b/examples/fold.ml
index 027c37ea47..b92774d853 100644
--- a/examples/fold.ml
+++ b/examples/fold.ml
@@ -62,11 +62,12 @@ end = struct
     | None -> failwith "no kind"
 end
 
-let main () =
+let main env =
   let ps name = Fmt.(pf stdout "\n%s\n" name) in
   ps "Demo of how tree folders visit nodes.";
   Eio.Switch.run @@ fun sw ->
-  let repo = Store.Repo.v ~sw config in
+  let fs = Eio.Stdenv.fs env in
+  let repo = Store.Repo.v ~sw ~fs config in
   let main_b = Store.main repo in
   Store.set_exn ~info:(info "add c1") main_b [ "c1" ] "c1";
   Store.set_exn ~info:(info "add c2") main_b [ "c2" ] "c2";
@@ -91,4 +92,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/irmin-pack/gc.ml b/examples/irmin-pack/gc.ml
index ad3d160e57..c626beab70 100644
--- a/examples/irmin-pack/gc.ml
+++ b/examples/irmin-pack/gc.ml
@@ -160,11 +160,13 @@ let run_gc domain_mgr config repo tracker =
   let () = Store.split repo in
   Tracker.mark_next_gc_commit tracker
 
-let run_experiment domain_mgr config =
+let run_experiment env config =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
+  let domain_mgr = Eio.Stdenv.domain_mgr env in
   let num_of_commits = 200_000 in
   let gc_every = 1_000 in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let tracker = Tracker.v () in
   (* Create commits *)
   let _ =
@@ -190,9 +192,7 @@ let run_experiment domain_mgr config =
 
 let () =
   Eio_main.run @@ fun env ->
-  let domain_mgr = Eio.Stdenv.domain_mgr env in
-  Irmin_pack_unix.Io.set_env (Eio.Stdenv.fs env);
   Printf.printf "== RUN 1: deleting discarded data ==\n";
-  run_experiment domain_mgr Repo_config.config;
+  run_experiment env Repo_config.config;
   Printf.printf "== RUN 2: archiving discarded data ==\n";
-  run_experiment domain_mgr Repo_config.config_with_lower
+  run_experiment env Repo_config.config_with_lower
diff --git a/examples/irmin-pack/kv.ml b/examples/irmin-pack/kv.ml
index 8f48978a69..7586d06a62 100644
--- a/examples/irmin-pack/kv.ml
+++ b/examples/irmin-pack/kv.ml
@@ -68,11 +68,12 @@ end
 module StoreMaker = Irmin_pack_unix.KV (Conf)
 module Store = StoreMaker.Make (Irmin.Contents.String)
 
-let main () =
+let main env =
   (* Create a switch *)
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   (* Instantiate a repository *)
-  let repo = Store.Repo.v ~sw Repo_config.config in
+  let repo = Store.Repo.v ~sw ~fs Repo_config.config in
 
   (* Get the store from the main branch. *)
   let store = Store.main repo in
@@ -96,6 +97,5 @@ let setup_logs () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Irmin_pack_unix.Io.set_env (Eio.Stdenv.fs env);
   setup_logs ();
-  main ()
+  main env
diff --git a/examples/irmin_git_store.ml b/examples/irmin_git_store.ml
index e29b7c1fb7..00949adfc7 100644
--- a/examples/irmin_git_store.ml
+++ b/examples/irmin_git_store.ml
@@ -30,11 +30,12 @@ let read_exn t k =
   print_endline msg;
   Store.get t k
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
   let config = Irmin_git.config ~bare:true Config.root in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.main repo in
   update t [ "root"; "misc"; "1.txt" ] "Hello world!";
   update t [ "root"; "misc"; "2.txt" ] "Hi!";
@@ -53,16 +54,16 @@ let main () =
       let _ = read_exn t [ "root"; "misc"; "3.txt" ] in
       ()
 
-let main () =
+let main env =
   Printf.printf
     "This example creates a Git repository in %s and use it to read \n\
      and write data:\n"
     Config.root;
   let _ = Sys.command (Printf.sprintf "rm -rf %s" Config.root) in
-  main ();
+  main env;
   Printf.printf "You can now run `cd %s && tig` to inspect the store.\n"
     Config.root
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/merkle_proofs.md b/examples/merkle_proofs.md
index 5f2e0f79ad..dacb87a991 100644
--- a/examples/merkle_proofs.md
+++ b/examples/merkle_proofs.md
@@ -29,6 +29,7 @@ module Store = Irmin_git_unix.FS.KV (Contents)
 let eio_run fn =
   Eio_main.run @@ fun env ->
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Lwt_eio.with_event_loop ~clock:env#clock (fn ~sw)
 ```
 
@@ -36,7 +37,7 @@ Open a repo.
 
 ```ocaml
 # let config = Irmin_git.config ~bare:true "./tmp-irmin/test"
-  let repo = eio_run @@ fun ~sw _ -> Store.Repo.v ~sw config;;
+  let repo = eio_run @@ fun ~sw _ -> Store.Repo.v ~sw ~fs config;;
 val config : Irmin.config = <abstr>
 val repo : Store.repo = <abstr>
 ```
diff --git a/examples/plugin/plugin.ml b/examples/plugin/plugin.ml
index c2af8f8cce..4f063f0328 100644
--- a/examples/plugin/plugin.ml
+++ b/examples/plugin/plugin.ml
@@ -48,7 +48,6 @@ let () =
   @@ Logs.Src.list ()
 
 let () =
-  Eio_main.run @@ fun env ->
-  Irmin_pack_unix.Io.set_env (Eio.Stdenv.fs env);
+  Eio_main.run @@ fun _env ->
   Resolver.Contents.add ~default:true "int" (module Int);
   Resolver.Store.add ~default:true "mem-int" (Fixed store)
diff --git a/examples/process.ml b/examples/process.ml
index a3497a59ad..be49b7e4ce 100644
--- a/examples/process.ml
+++ b/examples/process.ml
@@ -110,10 +110,11 @@ let info image message () =
 
 let main = branch images.(0)
 
-let init () =
+let init env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.of_branch repo main in
   Store.set_exn t ~info:(info images.(0) "init") [ "0" ] "0";
   List.iter
@@ -125,8 +126,9 @@ let init () =
 let random_array a = a.(Random.int (Array.length a))
 let random_list l = random_array (Array.of_list l)
 
-let rec process image =
+let rec process env image =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   let id = branch image in
   Printf.printf "Processing %s\n%!" id;
   let actions = random_list image.actions in
@@ -135,7 +137,7 @@ let rec process image =
     with _ ->
       ([ "log"; id; "0" ], fun () -> id ^ string_of_int (Random.int 10))
   in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.of_branch repo id in
   Store.set_exn t ~info:(info image actions.message) key (value ());
   let () =
@@ -153,7 +155,7 @@ let rec process image =
         | Error _ -> failwith "conflict!")
   in
   Eio_unix.sleep (max 0.1 (Random.float 0.3));
-  process image
+  process env image
 
 let rec protect fn x () =
   try fn x
@@ -166,10 +168,11 @@ let rec watchdog () =
   Eio_unix.sleep 1.;
   watchdog ()
 
-let main () =
-  init ();
-  Eio.Fiber.any (watchdog :: List.map (protect process) (Array.to_list images))
+let main env =
+  init env;
+  Eio.Fiber.any
+    (watchdog :: List.map (protect (process env)) (Array.to_list images))
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/push.ml b/examples/push.ml
index bc5c05df20..af245b9ef5 100644
--- a/examples/push.ml
+++ b/examples/push.ml
@@ -29,11 +29,12 @@ let headers =
   let e = Cohttp.Header.of_list [] in
   Cohttp.Header.add_authorization e (`Basic (user, token))
 
-let test () =
+let test env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
   let config = Irmin_git.config Config.root in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.main repo in
   let remote = Store.remote ~headers url () in
   let _ = Sync.pull_exn t remote `Set in
@@ -52,4 +53,4 @@ let test () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> test ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> test env
diff --git a/examples/readme.ml b/examples/readme.ml
index fffb45c670..948276053b 100644
--- a/examples/readme.ml
+++ b/examples/readme.ml
@@ -10,11 +10,12 @@ let author = "Example <example@example.com>"
 (* Commit information *)
 let info fmt = Irmin_git_unix.info ~author fmt
 
-let main () =
+let main env =
   (* Create the switch *)
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   (* Open the repo *)
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
 
   (* Load the main branch *)
   let t = Store.main repo in
@@ -29,4 +30,4 @@ let main () =
 (* Run the program *)
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env
diff --git a/examples/server.ml b/examples/server.ml
index 42574fc489..9f48d67d9d 100644
--- a/examples/server.ml
+++ b/examples/server.ml
@@ -20,24 +20,26 @@ module Server = Irmin_server_unix.Make (Store)
 
 let info () = Irmin.Info.Default.empty
 
-let init () =
+let init env =
   Eio.Switch.run @@ fun sw ->
-  let repo = Store.Repo.v ~sw (Irmin_mem.config ()) in
+  let fs = Eio.Stdenv.fs env in
+  let repo = Store.Repo.v ~sw ~fs (Irmin_mem.config ()) in
   let main = Store.main repo in
   Store.set_exn ~info main [ "foo" ] "bar"
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   let uri = Uri.of_string Sys.argv.(1) in
   let config = Irmin_mem.config () in
   let dashboard = `TCP (`Port 1234) in
   Lwt_eio.run_lwt @@ fun () ->
-  let* server = Server.v ~sw ~uri ~dashboard config in
+  let* server = Server.v ~sw ~fs ~uri ~dashboard config in
   Format.printf "Listening on %a@." Uri.pp uri;
   Server.serve server
 
 let () =
   Eio_main.run @@ fun env ->
   Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ ->
-  init ();
-  main ()
+  init env;
+  main env
diff --git a/examples/sync.ml b/examples/sync.ml
index 3e5cac7daa..da7681f745 100644
--- a/examples/sync.ml
+++ b/examples/sync.ml
@@ -23,11 +23,12 @@ let path =
 module Store = Irmin_git_unix.FS.KV (Irmin.Contents.String)
 module Sync = Irmin.Sync.Make (Store)
 
-let test () =
+let test env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
   let config = Irmin_git.config Config.root in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.of_branch repo "master" in
   let upstream = Store.remote path () in
   let _ = Sync.pull_exn t upstream `Set in
@@ -40,4 +41,4 @@ let test () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> test ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> test env
diff --git a/examples/trees.ml b/examples/trees.ml
index 9f4f478ad2..e94fd4e9ab 100644
--- a/examples/trees.ml
+++ b/examples/trees.ml
@@ -50,15 +50,16 @@ let t_of_tree v =
   let t2s = List.rev (List.sort compare t2s) in
   List.fold_left aux [] t2s
 
-let main () =
+let main env =
   Eio.Switch.run @@ fun sw ->
+  let fs = Eio.Stdenv.fs env in
   Config.init ();
   let config = Irmin_git.config ~bare:false Config.root in
   let t =
     [ { x = "foo"; y = 3 }; { x = "bar"; y = 5 }; { x = "too"; y = 10 } ]
   in
   let v = tree_of_t t in
-  let repo = Store.Repo.v ~sw config in
+  let repo = Store.Repo.v ~sw ~fs config in
   let t = Store.main repo in
   Store.set_tree_exn t ~info:(info "update a/b") [ "a"; "b" ] v;
   let v = Store.get_tree t [ "a"; "b" ] in
@@ -70,4 +71,4 @@ let main () =
 
 let () =
   Eio_main.run @@ fun env ->
-  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main ()
+  Lwt_eio.with_event_loop ~clock:env#clock @@ fun _ -> main env