diff --git a/src/dune_rules/cm_files.ml b/src/dune_rules/cm_files.ml
index 113955fc74a0..8b6013915259 100644
--- a/src/dune_rules/cm_files.ml
+++ b/src/dune_rules/cm_files.ml
@@ -40,6 +40,11 @@ let top_sorted_cms t ~mode =
     Obj_dir.Module.L.cm_files t.obj_dir ~kind:(Ocaml kind) modules)
 ;;
 
+let top_sorted_modules t =
+  Action_builder.map t.top_sorted_modules ~f:(fun modules ->
+    filter_excluded_modules t modules)
+;;
+
 let top_sorted_objects_and_cms t ~mode =
   Action_builder.map t.top_sorted_modules ~f:(fun modules ->
     let modules = filter_excluded_modules t modules in
diff --git a/src/dune_rules/cm_files.mli b/src/dune_rules/cm_files.mli
index be3cc69b33d6..62ea0f532399 100644
--- a/src/dune_rules/cm_files.mli
+++ b/src/dune_rules/cm_files.mli
@@ -17,4 +17,5 @@ val make
 
 val unsorted_objects_and_cms : t -> mode:Mode.t -> Path.t list
 val top_sorted_cms : t -> mode:Mode.t -> Path.t list Action_builder.t
+val top_sorted_modules : t -> Module.t list Action_builder.t
 val top_sorted_objects_and_cms : t -> mode:Mode.t -> Path.t list Action_builder.t
diff --git a/src/dune_rules/dune_file.mli b/src/dune_rules/dune_file.mli
index 11a27a76c725..d0ac3c108629 100644
--- a/src/dune_rules/dune_file.mli
+++ b/src/dune_rules/dune_file.mli
@@ -200,6 +200,7 @@ module Library : sig
       declared in. *)
   val archive : t -> dir:Path.Build.t -> ext:string -> Path.Build.t
 
+  val archive_basename : t -> ext:string -> string
   val best_name : t -> Lib_name.t
   val is_virtual : t -> bool
   val is_impl : t -> bool
diff --git a/src/dune_rules/jsoo/jsoo_rules.ml b/src/dune_rules/jsoo/jsoo_rules.ml
index 2b5cf0c82137..c004506d5280 100644
--- a/src/dune_rules/jsoo/jsoo_rules.ml
+++ b/src/dune_rules/jsoo/jsoo_rules.ml
@@ -7,7 +7,7 @@ module Config : sig
   val path : t -> string
   val of_string : string -> t
   val of_flags : string list -> t
-  val to_flags : t -> string list
+  val to_flags : current:string list -> t -> string list
 end = struct
   type t =
     { js_string : bool option
@@ -80,12 +80,15 @@ end = struct
     loop default l
   ;;
 
-  let to_flags t =
-    List.concat_map (get t) ~f:(function
-      | "toplevel", true -> [ "--toplevel" ]
+  let to_flags ~current t =
+    current
+    :: List.map (get t) ~f:(function
+      | "toplevel", true ->
+        if List.mem current "--toplevel" ~equal:String.equal then [] else [ "--toplevel" ]
       | "toplevel", false -> []
       | name, true -> [ "--enable"; name ]
       | name, false -> [ "--disable"; name ])
+    |> List.concat
   ;;
 end
 
@@ -191,6 +194,12 @@ let js_of_ocaml_rule
   let open Memo.O in
   let+ jsoo = jsoo ~dir sctx
   and+ flags = js_of_ocaml_flags sctx ~dir flags in
+  let flags =
+    match sub_command with
+    | Compile -> flags.compile
+    | Link -> flags.link
+    | Build_runtime -> flags.build_runtime
+  in
   Command.run
     ~dir:(Path.build dir)
     jsoo
@@ -198,18 +207,17 @@ let js_of_ocaml_rule
        | Compile -> S []
        | Link -> A "link"
        | Build_runtime -> A "build-runtime")
-    ; Command.Args.dyn
-        (match sub_command with
-         | Compile -> flags.compile
-         | Link -> flags.link
-         | Build_runtime -> flags.build_runtime)
     ; (match config with
-       | None -> S []
+       | None ->
+         Dyn
+           (Action_builder.map flags ~f:(fun flags ->
+              Command.Args.S (List.map flags ~f:(fun x -> Command.Args.A x))))
        | Some config ->
          Dyn
-           (Action_builder.map config ~f:(fun config ->
+           (Action_builder.map2 flags config ~f:(fun flags config ->
               Command.Args.S
-                (List.map (Config.to_flags config) ~f:(fun x -> Command.Args.A x)))))
+                (List.map (Config.to_flags ~current:flags config) ~f:(fun x ->
+                   Command.Args.A x)))))
     ; A "-o"
     ; Target target
     ; spec
@@ -315,12 +323,13 @@ let link_rule cc ~runtime ~target ~obj_dir cm ~flags ~linkall ~link_time_code_ge
     let special_units =
       List.concat_map to_link ~f:(function
         | Lib_flags.Lib_and_module.Lib _lib -> []
-        | Module (obj_dir, m) -> [ in_obj_dir' ~obj_dir ~config:None [ mod_name m ] ])
+        | Module (obj_dir, m) ->
+          [ in_obj_dir' ~obj_dir ~config:(Some config) [ mod_name m ] ])
     in
     let all_libs = List.concat_map libs ~f:(jsoo_archives ctx config) in
     let all_other_modules =
       List.map cm ~f:(fun m ->
-        Path.build (in_obj_dir ~obj_dir ~config:None [ mod_name m ]))
+        Path.build (in_obj_dir ~obj_dir ~config:(Some config) [ mod_name m ]))
     in
     let std_exit =
       Path.build (in_build_dir ctx ~config [ "stdlib"; "std_exit" ^ Js_of_ocaml.Ext.cmo ])
@@ -361,6 +370,33 @@ let build_cm sctx ~dir ~in_context ~src ~obj_dir ~config =
     ~config:(Option.map config ~f:Action_builder.return)
 ;;
 
+let build_cma_js sctx ~dir ~in_context ~obj_dir ~config ~linkall:_ cm_files name =
+  let target = in_obj_dir ~obj_dir ~config [ name ] in
+  let flags = in_context.Js_of_ocaml.In_context.flags in
+  let modules =
+    let open Action_builder.O in
+    let+ l = Cm_files.top_sorted_modules cm_files in
+    let l =
+      List.map l ~f:(fun m ->
+        in_obj_dir
+          ~obj_dir
+          ~config
+          [ Module_name.Unique.to_string (Module.obj_name m) ^ Js_of_ocaml.Ext.cmo ]
+        |> Path.build)
+    in
+    l
+  in
+  js_of_ocaml_rule
+    sctx
+    ~dir
+    ~sub_command:Link
+    ~config:(Option.map config ~f:Action_builder.return)
+    ~flags
+    ~spec:
+      (S [ A "-a"; Dyn (Action_builder.map modules ~f:(fun x -> Command.Args.Deps x)) ])
+    ~target
+;;
+
 let setup_separate_compilation_rules sctx components =
   match components with
   | _ :: _ :: _ :: _ | [] | [ _ ] -> Memo.return ()
diff --git a/src/dune_rules/jsoo/jsoo_rules.mli b/src/dune_rules/jsoo/jsoo_rules.mli
index dcb7fa414609..6cd8600a5565 100644
--- a/src/dune_rules/jsoo/jsoo_rules.mli
+++ b/src/dune_rules/jsoo/jsoo_rules.mli
@@ -36,6 +36,17 @@ val build_exe
   -> link_time_code_gen:Link_time_code_gen_type.t Resolve.t
   -> unit Memo.t
 
+val build_cma_js
+  :  Super_context.t
+  -> dir:Path.Build.t
+  -> in_context:Js_of_ocaml.In_context.t
+  -> obj_dir:Path.Build.t Obj_dir.t
+  -> config:Config.t option
+  -> linkall:bool Action_builder.t
+  -> Cm_files.t
+  -> string
+  -> Action.Full.t Action_builder.With_targets.t Memo.t
+
 val setup_separate_compilation_rules : Super_context.t -> string list -> unit Memo.t
 val runner : string
 val js_of_ocaml_runtest_alias : Super_context.t -> dir:Path.Build.t -> Alias.Name.t Memo.t
diff --git a/src/dune_rules/lib_rules.ml b/src/dune_rules/lib_rules.ml
index b362c67b72a1..eb6375342386 100644
--- a/src/dune_rules/lib_rules.ml
+++ b/src/dune_rules/lib_rules.ml
@@ -120,6 +120,41 @@ let build_lib
              ]))
 ;;
 
+(* Build an OCaml library. *)
+let build_js_lib
+  (lib : Library.t)
+  ~sctx
+  ~expander
+  ~flags
+  ~dir
+  ~cm_files
+  ~in_context
+  ~obj_dir
+  config
+  =
+  let linkall =
+    match lib.kind with
+    | Ppx_deriver _ | Ppx_rewriter _ -> Action_builder.return true
+    | Normal ->
+      let standard = Action_builder.return [] in
+      let open Action_builder.O in
+      let+ library_flags =
+        Expander.expand_and_eval_set expander lib.library_flags ~standard
+      and+ ocaml_flags = Ocaml_flags.get flags (Ocaml Byte) in
+      List.exists library_flags ~f:(String.equal "-linkall")
+      || List.exists ocaml_flags ~f:(String.equal "-linkall")
+  in
+  Jsoo_rules.build_cma_js
+    sctx
+    ~dir
+    ~config
+    ~in_context
+    ~obj_dir
+    ~linkall
+    cm_files
+    (Library.archive_basename lib ~ext:".cma.js")
+;;
+
 let gen_wrapped_compat_modules (lib : Library.t) cctx =
   let modules = Compilation_context.modules cctx in
   let wrapped_compat = Modules.wrapped_compat modules in
@@ -484,20 +519,39 @@ let setup_build_archives
       build_lib lib ~native_archives ~dir ~sctx ~expander ~flags ~mode ~cm_files)
   and* () =
     (* Build *.cma.js *)
-    Memo.when_ modes.ocaml.byte (fun () ->
-      let src = Library.archive lib ~dir ~ext:(Mode.compiled_lib_ext Mode.Byte) in
-      let action_with_targets =
-        List.map Jsoo_rules.Config.all ~f:(fun config ->
-          Jsoo_rules.build_cm
-            sctx
-            ~dir
-            ~in_context:js_of_ocaml
-            ~config:(Some config)
-            ~src:(Path.build src)
-            ~obj_dir)
-      in
-      Memo.parallel_iter action_with_targets ~f:(fun rule ->
-        rule >>= Super_context.add_rule sctx ~dir ~loc:lib.buildable.loc))
+    match `From_cmos with
+    | `From_cma ->
+      Memo.when_ modes.ocaml.byte (fun () ->
+        let src = Library.archive lib ~dir ~ext:(Mode.compiled_lib_ext Mode.Byte) in
+        let action_with_targets =
+          List.map Jsoo_rules.Config.all ~f:(fun config ->
+            Jsoo_rules.build_cm
+              sctx
+              ~dir
+              ~in_context:js_of_ocaml
+              ~config:(Some config)
+              ~src:(Path.build src)
+              ~obj_dir)
+        in
+        Memo.parallel_iter action_with_targets ~f:(fun rule ->
+          rule >>= Super_context.add_rule sctx ~dir ~loc:lib.buildable.loc))
+    | `From_cmos ->
+      Memo.when_ modes.ocaml.byte (fun () ->
+        let action_with_targets =
+          List.map Jsoo_rules.Config.all ~f:(fun config ->
+            build_js_lib
+              (lib : Library.t)
+              ~sctx
+              ~expander
+              ~flags
+              ~dir
+              ~cm_files
+              ~in_context:js_of_ocaml
+              ~obj_dir
+              (Some config))
+        in
+        Memo.parallel_iter action_with_targets ~f:(fun rule ->
+          rule >>= Super_context.add_rule sctx ~dir ~loc:lib.buildable.loc))
   in
   Memo.when_
     (Dynlink_supported.By_the_os.get natdynlink_supported && modes.ocaml.native)
diff --git a/src/dune_rules/module_compilation.ml b/src/dune_rules/module_compilation.ml
index 6544ff9a0c3e..fc88d83f5aab 100644
--- a/src/dune_rules/module_compilation.ml
+++ b/src/dune_rules/module_compilation.ml
@@ -315,15 +315,17 @@ let build_module ?(force_write_cmi = false) ?(precompiled_cmi = false) cctx m =
           let sctx = Compilation_context.super_context cctx in
           let dir = Compilation_context.dir cctx in
           let action_with_targets =
-            Jsoo_rules.build_cm
-              sctx
-              ~dir
-              ~in_context
-              ~src:(Path.build src)
-              ~obj_dir
-              ~config:None
+            List.map Jsoo_rules.Config.all ~f:(fun config ->
+              Jsoo_rules.build_cm
+                sctx
+                ~dir
+                ~in_context
+                ~src:(Path.build src)
+                ~obj_dir
+                ~config:(Some config))
           in
-          action_with_targets >>= Super_context.add_rule sctx ~dir))
+          Memo.parallel_iter action_with_targets ~f:(fun rule ->
+            rule >>= Super_context.add_rule sctx ~dir)))
   in
   Memo.when_ melange (fun () ->
     let* () = build_cm ~cm_kind:(Melange Cmj) ~phase:None in
diff --git a/test/blackbox-tests/test-cases/jsoo/explicit-js-mode-specified.t/run.t b/test/blackbox-tests/test-cases/jsoo/explicit-js-mode-specified.t/run.t
index 6b9460d9b141..8924d6250573 100644
--- a/test/blackbox-tests/test-cases/jsoo/explicit-js-mode-specified.t/run.t
+++ b/test/blackbox-tests/test-cases/jsoo/explicit-js-mode-specified.t/run.t
@@ -11,7 +11,7 @@ Check that .bc.js rule is generated only if js mode is used.
         ocamlc .b.eobjs/byte/b.{cmi,cmo,cmt}
    js_of_ocaml .js/default/stdlib/std_exit.cmo.js
    js_of_ocaml .js/default/stdlib/stdlib.cma.js
-   js_of_ocaml .b.eobjs/jsoo/b.cmo.js
+   js_of_ocaml .b.eobjs/jsoo/default/b.cmo.js
    js_of_ocaml b.bc.js
 
 We also check that .cmo.js rules are not generated if not specified.
@@ -24,10 +24,11 @@ JS compilation of libraries is always available to avoid having to annotate
 every dependency of an executable.
 
   $ dune build --display short _build/default/.foo.objs/jsoo/default/foo.cma.js
-        ocamlc .foo.objs/byte/foo.{cmi,cmo,cmt}
       ocamldep .foo.objs/foo__C.impl.d
+        ocamlc .foo.objs/byte/foo.{cmi,cmo,cmt}
+   js_of_ocaml .foo.objs/jsoo/default/foo.cmo.js
         ocamlc .foo.objs/byte/foo__C.{cmi,cmo,cmt}
-        ocamlc foo.cma
+   js_of_ocaml .foo.objs/jsoo/default/foo__C.cmo.js
    js_of_ocaml .foo.objs/jsoo/default/foo.cma.js
 
 Check that js targets are attached to @all, but not for tests that do not
@@ -39,10 +40,12 @@ specify js mode (#1940).
    js_of_ocaml .e.eobjs/jsoo/e.bc.runtime.js
    js_of_ocaml .js/default/stdlib/std_exit.cmo.js
    js_of_ocaml .js/default/stdlib/stdlib.cma.js
-   js_of_ocaml .b.eobjs/jsoo/b.cmo.js
+   js_of_ocaml .foo.objs/jsoo/default/foo.cmo.js
+   js_of_ocaml .b.eobjs/jsoo/default/b.cmo.js
+   js_of_ocaml .foo.objs/jsoo/default/foo__C.cmo.js
    js_of_ocaml b.bc.js
    js_of_ocaml .foo.objs/jsoo/default/foo.cma.js
-   js_of_ocaml .e.eobjs/jsoo/e.cmo.js
+   js_of_ocaml .e.eobjs/jsoo/default/e.cmo.js
    js_of_ocaml e.bc.js
 
 Check that building a JS-enabled executable that depends on a library works.
@@ -56,8 +59,9 @@ Check that building a JS-enabled executable that depends on a library works.
    js_of_ocaml .js/default/stdlib/std_exit.cmo.js
    js_of_ocaml .js/default/stdlib/stdlib.cma.js
         ocamlc .foo.objs/byte/foo__C.{cmi,cmo,cmt}
+   js_of_ocaml .foo.objs/jsoo/default/foo.cmo.js
         ocamlc .e.eobjs/byte/e.{cmi,cmo,cmt}
-        ocamlc foo.cma
-   js_of_ocaml .e.eobjs/jsoo/e.cmo.js
+   js_of_ocaml .foo.objs/jsoo/default/foo__C.cmo.js
+   js_of_ocaml .e.eobjs/jsoo/default/e.cmo.js
    js_of_ocaml .foo.objs/jsoo/default/foo.cma.js
    js_of_ocaml e.bc.js
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config.t/run.t b/test/blackbox-tests/test-cases/jsoo/jsoo-config.t/run.t
index 95d85a917c1e..f6b532dc84a2 100644
--- a/test/blackbox-tests/test-cases/jsoo/jsoo-config.t/run.t
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config.t/run.t
@@ -1,6 +1,34 @@
 tests js_of_ocaml conigs
 
-  $ dune build bin/bin1.bc.js bin/bin2.bc.js bin/bin3.bc.js
+  $ dune build bin/bin1.bc.js bin/bin2.bc.js bin/bin3.bc.js --display short
+   js_of_ocaml bin/.bin1.eobjs/jsoo/bin1.bc.runtime.js
+   js_of_ocaml bin/.bin2.eobjs/jsoo/bin2.bc.runtime.js
+   js_of_ocaml bin/.bin3.eobjs/jsoo/bin3.bc.runtime.js
+   js_of_ocaml .js/use-js-string/stdlib/std_exit.cmo.js
+   js_of_ocaml .js/use-js-string/stdlib/stdlib.cma.js
+        ocamlc lib/.library1.objs/byte/library1.{cmi,cmo,cmt}
+   js_of_ocaml .js/!use-js-string/stdlib/std_exit.cmo.js
+   js_of_ocaml .js/!use-js-string/stdlib/stdlib.cma.js
+   js_of_ocaml .js/default/stdlib/std_exit.cmo.js
+   js_of_ocaml .js/default/stdlib/stdlib.cma.js
+        ocamlc bin/.bin1.eobjs/byte/dune__exe__Bin1.{cmi,cmti}
+   js_of_ocaml lib/.library1.objs/jsoo/use-js-string/library1.cmo.js
+        ocamlc bin/.bin2.eobjs/byte/dune__exe__Bin2.{cmi,cmti}
+   js_of_ocaml lib/.library1.objs/jsoo/!use-js-string/library1.cmo.js
+   js_of_ocaml lib/.library1.objs/jsoo/default/library1.cmo.js
+        ocamlc bin/.bin3.eobjs/byte/dune__exe__Bin3.{cmi,cmti}
+        ocamlc bin/.bin1.eobjs/byte/dune__exe__Bin1.{cmo,cmt}
+   js_of_ocaml lib/.library1.objs/jsoo/use-js-string/library1.cma.js
+        ocamlc bin/.bin2.eobjs/byte/dune__exe__Bin2.{cmo,cmt}
+   js_of_ocaml lib/.library1.objs/jsoo/!use-js-string/library1.cma.js
+   js_of_ocaml lib/.library1.objs/jsoo/default/library1.cma.js
+        ocamlc bin/.bin3.eobjs/byte/dune__exe__Bin3.{cmo,cmt}
+   js_of_ocaml bin/.bin1.eobjs/jsoo/use-js-string/dune__exe__Bin1.cmo.js
+   js_of_ocaml bin/.bin2.eobjs/jsoo/!use-js-string/dune__exe__Bin2.cmo.js
+   js_of_ocaml bin/.bin3.eobjs/jsoo/default/dune__exe__Bin3.cmo.js
+   js_of_ocaml bin/bin1.bc.js
+   js_of_ocaml bin/bin2.bc.js
+   js_of_ocaml bin/bin3.bc.js
   $ node _build/default/bin/bin1.bc.js
   Hello bin1
   Hi library1
diff --git a/test/blackbox-tests/test-cases/jsoo/no-check-prim.t/run.t b/test/blackbox-tests/test-cases/jsoo/no-check-prim.t/run.t
index 33fc4afab30e..78af37931ae7 100644
--- a/test/blackbox-tests/test-cases/jsoo/no-check-prim.t/run.t
+++ b/test/blackbox-tests/test-cases/jsoo/no-check-prim.t/run.t
@@ -14,17 +14,20 @@ Compilation using jsoo
    js_of_ocaml .js/default/js_of_ocaml/js_of_ocaml.cma.js
    js_of_ocaml .js/default/stdlib/std_exit.cmo.js
    js_of_ocaml .js/default/stdlib/stdlib.cma.js
+   js_of_ocaml lib/.x.objs/jsoo/default/x__.cmo.js
       ocamlopt lib/.x.objs/native/x__Y.{cmx,o}
         ocamlc lib/.x.objs/byte/x.{cmi,cmo,cmt}
+   js_of_ocaml lib/.x.objs/jsoo/default/x__Y.cmo.js
       ocamlopt lib/.x.objs/native/x.{cmx,o}
         ocamlc bin/.technologic.eobjs/byte/z.{cmi,cmo,cmt}
         ocamlc lib/x.cma
+   js_of_ocaml lib/.x.objs/jsoo/default/x.cmo.js
       ocamlopt lib/x.{a,cmxa}
         ocamlc bin/.technologic.eobjs/byte/technologic.{cmi,cmo,cmt}
-   js_of_ocaml bin/.technologic.eobjs/jsoo/z.cmo.js
+   js_of_ocaml bin/.technologic.eobjs/jsoo/default/z.cmo.js
    js_of_ocaml lib/.x.objs/jsoo/default/x.cma.js
       ocamlopt lib/x.cmxs
-   js_of_ocaml bin/.technologic.eobjs/jsoo/technologic.cmo.js
+   js_of_ocaml bin/.technologic.eobjs/jsoo/default/technologic.cmo.js
    js_of_ocaml bin/technologic.bc.js
   $ node ./_build/default/bin/technologic.bc.js
   buy it
diff --git a/test/blackbox-tests/test-cases/jsoo/public-libs.t/run.t b/test/blackbox-tests/test-cases/jsoo/public-libs.t/run.t
index bb44601c9c9e..c7908d2b2ed8 100644
--- a/test/blackbox-tests/test-cases/jsoo/public-libs.t/run.t
+++ b/test/blackbox-tests/test-cases/jsoo/public-libs.t/run.t
@@ -8,10 +8,11 @@ Compilation of libraries with pulic-names
         ocamlc a/a.cma
    js_of_ocaml .js/default/stdlib/std_exit.cmo.js
    js_of_ocaml .js/default/stdlib/stdlib.cma.js
+   js_of_ocaml a/.a.objs/jsoo/default/a.cmo.js
       ocamlopt a/a.{a,cmxa}
         ocamlc b/.main.eobjs/byte/dune__exe__Main.{cmo,cmt}
    js_of_ocaml a/.a.objs/jsoo/default/a.cma.js
       ocamlopt a/a.cmxs
         ocamlc b/main.bc-for-jsoo
-   js_of_ocaml b/.main.eobjs/jsoo/dune__exe__Main.cmo.js
+   js_of_ocaml b/.main.eobjs/jsoo/default/dune__exe__Main.cmo.js
    js_of_ocaml b/main.bc.js