diff --git a/src/dune_rules/jsoo/jsoo_rules.ml b/src/dune_rules/jsoo/jsoo_rules.ml
index e65879f040e..8317a3620db 100644
--- a/src/dune_rules/jsoo/jsoo_rules.ml
+++ b/src/dune_rules/jsoo/jsoo_rules.ml
@@ -41,6 +41,50 @@ let js_env = compute_env ~mode:JS
 let wasm_env = compute_env ~mode:Wasm
 let jsoo_env ~dir ~mode = (Js_of_ocaml.Mode.select ~mode ~js:js_env ~wasm:wasm_env) ~dir
 
+module Version = struct
+  type t = int * int
+
+  let of_string s : t option =
+    let s =
+      match
+        String.findi s ~f:(function
+          | '+' | '-' | '~' -> true
+          | _ -> false)
+      with
+      | None -> s
+      | Some i -> String.take s i
+    in
+    try
+      match String.split s ~on:'.' with
+      | [] -> None
+      | [ major ] -> Some (int_of_string major, 0)
+      | major :: minor :: _ -> Some (int_of_string major, int_of_string minor)
+    with
+    | _ -> None
+  ;;
+
+  let compare (ma1, mi1) (ma2, mi2) =
+    match Int.compare ma1 ma2 with
+    | Eq -> Int.compare mi1 mi2
+    | n -> n
+  ;;
+
+  let impl_version bin =
+    let* _ = Build_system.build_file bin in
+    Memo.of_reproducible_fiber
+    @@ Process.run_capture_line ~display:Quiet Strict bin [ "--version" ]
+    |> Memo.map ~f:of_string
+  ;;
+
+  let version_memo = Memo.create "jsoo-version" ~input:(module Path) impl_version
+
+  let jsoo_version jsoo =
+    match jsoo with
+    | Ok jsoo_path -> Memo.exec version_memo jsoo_path
+    | Error e -> Action.Prog.Not_found.raise e
+  ;;
+end
+
 module Config : sig
   type t
 
@@ -48,48 +92,75 @@ 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 : jsoo_version:Version.t option -> t -> string list
+  val remove_config_flags : string list -> string list
 end = struct
+  type effects_backend =
+    | Cps
+    | Double_translation
+
   type t =
     { js_string : bool option
-    ; effects : bool option
+    ; effects : effects_backend option
     ; toplevel : bool option
     }
 
   let default = { js_string = None; effects = None; toplevel = None }
   let bool_opt = [ None; Some true; Some false ]
+  let effects_opt = [ None; Some Cps; Some Double_translation ]
 
   let all =
     List.concat_map bool_opt ~f:(fun js_string ->
-      List.concat_map bool_opt ~f:(fun effects ->
+      List.concat_map effects_opt ~f:(fun effects ->
         List.concat_map bool_opt ~f:(fun toplevel -> [ { js_string; effects; toplevel } ])))
   ;;
 
-  let get t =
-    List.filter_map
-      [ "use-js-string", t.js_string; "effects", t.effects; "toplevel", t.toplevel ]
-      ~f:(fun (n, v) ->
-        match v with
-        | None -> None
-        | Some v -> Some (n, v))
+  let enable name acc =
+    match name with
+    | "use-js-string" -> { acc with js_string = Some true }
+    | "effects" ->
+      (* [--enable effects], used alone, implies [--effects=cps] *)
+      (match acc.effects with
+       | None -> { acc with effects = Some Cps }
+       | Some _ -> acc)
+    | "toplevel" -> { acc with toplevel = Some true }
+    | _ -> acc
   ;;
 
-  let set acc name v =
+  let disable name acc =
     match name with
-    | "use-js-string" -> { acc with js_string = Some v }
-    | "effects" -> { acc with effects = Some v }
-    | "toplevel" -> { acc with toplevel = Some v }
+    | "use-js-string" -> { acc with js_string = Some false }
+    | "effects" -> { acc with effects = None }
+    | "toplevel" -> { acc with toplevel = Some false }
     | _ -> acc
   ;;
 
+  let string_of_effects = function
+    | Cps -> "cps"
+    | Double_translation -> "double-translation"
+  ;;
+
   let path t =
     if t = default
     then "default"
-    else
-      List.map (get t) ~f:(function
-        | x, true -> x
-        | x, false -> "!" ^ x)
-      |> String.concat ~sep:"+"
+    else (
+      let of_bool_opt key =
+        Option.map ~f:(function
+          | true -> key
+          | false -> "!" ^ key)
+      in
+      List.filter_opt
+        [ of_bool_opt "use-js-string" t.js_string
+        ; Option.map t.effects ~f:(fun e -> "effects=" ^ string_of_effects e)
+        ; of_bool_opt "toplevel" t.toplevel
+        ]
+      |> String.concat ~sep:"+")
+  ;;
+
+  let effects_of_string = function
+    | "cps" -> Some Cps
+    | "double-translation" -> Some Double_translation
+    | _ -> None
   ;;
 
   let of_string x =
@@ -97,80 +168,105 @@ end = struct
     | "default" -> default
     | _ ->
       List.fold_left (String.split ~on:'+' x) ~init:default ~f:(fun acc name ->
-        match String.drop_prefix ~prefix:"!" name with
-        | Some name -> set acc name false
-        | None -> set acc name true)
+        match
+          String.drop_prefix ~prefix:"!" name, String.drop_prefix ~prefix:"effects=" name
+        with
+        | Some name, _ -> disable name acc
+        | None, None -> enable name acc
+        | None, Some backend ->
+          (match effects_of_string backend with
+           | Some backend -> { acc with effects = Some backend }
+           | None -> acc))
   ;;
 
   let of_flags l =
     let rec loop acc = function
       | [] -> acc
-      | "--enable" :: name :: rest -> loop (set acc name true) rest
+      | "--enable" :: name :: rest -> loop (enable name acc) rest
       | maybe_enable :: rest when String.is_prefix maybe_enable ~prefix:"--enable=" ->
         (match String.drop_prefix maybe_enable ~prefix:"--enable=" with
-         | Some name -> loop (set acc name true) rest
+         | Some name -> loop (enable name acc) rest
          | _ -> assert false)
-      | "--disable" :: name :: rest -> loop (set acc name false) rest
+      | "--disable" :: name :: rest -> loop (disable name acc) rest
       | maybe_disable :: rest when String.is_prefix maybe_disable ~prefix:"--disable=" ->
         (match String.drop_prefix maybe_disable ~prefix:"--disable=" with
-         | Some name -> loop (set acc name false) rest
+         | Some name -> loop (disable name acc) rest
          | _ -> assert false)
-      | "--toplevel" :: rest -> loop (set acc "toplevel" true) rest
+      | "--toplevel" :: rest -> loop (enable "toplevel" acc) rest
+      | "--effects" :: "cps" :: rest -> loop { acc with effects = Some Cps } rest
+      | "--effects" :: "double-translation" :: rest ->
+        loop { acc with effects = Some Double_translation } rest
+      | maybe_effects :: rest when String.is_prefix maybe_effects ~prefix:"--effects=" ->
+        let backend =
+          Option.bind
+            (String.drop_prefix maybe_effects ~prefix:"--effects=")
+            ~f:effects_of_string
+        in
+        (match backend with
+         | Some backend -> loop { acc with effects = Some backend } rest
+         | None -> loop acc rest)
       | _ :: rest -> loop acc rest
     in
     loop default l
   ;;
 
-  let to_flags t =
-    List.concat_map (get t) ~f:(function
-      | "toplevel", true -> [ "--toplevel" ]
-      | "toplevel", false -> []
-      | name, true -> [ "--enable"; name ]
-      | name, false -> [ "--disable"; name ])
-  ;;
-end
-
-module Version = struct
-  type t = int * int
-
-  let of_string s : t option =
-    let s =
-      match
-        String.findi s ~f:(function
-          | '+' | '-' | '~' -> true
-          | _ -> false)
-      with
-      | None -> s
-      | Some i -> String.take s i
-    in
-    try
-      match String.split s ~on:'.' with
-      | [] -> None
-      | [ major ] -> Some (int_of_string major, 0)
-      | major :: minor :: _ -> Some (int_of_string major, int_of_string minor)
-    with
-    | _ -> None
+  let backward_compatible_effects ~jsoo_version str =
+    match str with
+    | None ->
+      (* For jsoo, this means unsupported effects. For wasmoo, this means effects go
+         through the Javascript Promise API. *)
+      None
+    | Some Cps ->
+      let v6_or_higher =
+        match jsoo_version with
+        | Some v ->
+          (match Version.compare v (6, 0) with
+           | Gt | Eq -> true
+           | Lt -> false)
+        | None -> false
+      in
+      if v6_or_higher then Some "--effects=cps" else Some "--enable=effects"
+    | Some Double_translation ->
+      (* For js_of_ocaml < 6.0, this flag does not exist and will raise an error,
+         which is fine. *)
+      Some "--effects=double-translation"
   ;;
 
-  let compare (ma1, mi1) (ma2, mi2) =
-    match Int.compare ma1 ma2 with
-    | Eq -> Int.compare mi1 mi2
-    | n -> n
-  ;;
-
-  let impl_version bin =
-    let* _ = Build_system.build_file bin in
-    Memo.of_reproducible_fiber
-    @@ Process.run_capture_line ~display:Quiet Strict bin [ "--version" ]
-    |> Memo.map ~f:of_string
+  let to_flags ~jsoo_version t =
+    List.filter_opt
+      [ (match t.toplevel with
+         | Some true -> Some "--toplevel"
+         | _ -> None)
+      ; backward_compatible_effects ~jsoo_version t.effects
+      ; (match t.js_string with
+         | Some true -> Some "--enable=use-js-string"
+         | Some false -> Some "--disable=use-js-string"
+         | None -> None)
+      ]
   ;;
 
-  let version_memo = Memo.create "jsoo-version" ~input:(module Path) impl_version
-
-  let jsoo_version jsoo =
-    match jsoo with
-    | Ok jsoo_path -> Memo.exec version_memo jsoo_path
-    | Error e -> Action.Prog.Not_found.raise e
+  let remove_config_flags flags =
+    let rec loop acc = function
+      | [] -> acc
+      | "--enable" :: ("effects" | "use-js-string") :: rest -> loop acc rest
+      | maybe_enable :: rest when String.is_prefix maybe_enable ~prefix:"--enable=" ->
+        (match String.drop_prefix maybe_enable ~prefix:"--enable=" with
+         | Some ("effects" | "use-js-string") -> loop acc rest
+         | Some _ -> loop (maybe_enable :: acc) rest
+         | None -> assert false)
+      | "--disable" :: ("effects" | "use-js-string") :: rest -> loop acc rest
+      | maybe_disable :: rest when String.is_prefix maybe_disable ~prefix:"--disable=" ->
+        (match String.drop_prefix maybe_disable ~prefix:"--disable=" with
+         | Some ("effects" | "use-js-string") -> loop acc rest
+         | Some _ -> loop (maybe_disable :: acc) rest
+         | None -> assert false)
+      | "--effects" :: _backend :: rest -> loop acc rest
+      | maybe_effects :: rest when String.is_prefix maybe_effects ~prefix:"--effects=" ->
+        loop acc rest
+      | "--toplevel" :: rest -> loop acc rest
+      | other :: rest -> loop (other :: acc) rest
+    in
+    loop [] flags |> List.rev
   ;;
 end
 
@@ -259,6 +355,13 @@ let js_of_ocaml_rule
     | Link -> flags.link
     | Build_runtime -> flags.build_runtime
   in
+  let flags =
+    (* Avoid duplicating flags that are covered by the config *)
+    Action_builder.map flags ~f:(fun flags ->
+      match config with
+      | None -> flags
+      | Some _ -> Config.remove_config_flags flags)
+  in
   Command.run_dyn_prog
     ~dir:(Path.build dir)
     jsoo
@@ -280,9 +383,14 @@ let js_of_ocaml_rule
        | None -> S []
        | Some config ->
          Dyn
-           (Action_builder.map config ~f:(fun config ->
-              Command.Args.S
-                (List.map (Config.to_flags config) ~f:(fun x -> Command.Args.A x)))))
+           (let+ config = config
+            and+ jsoo_version =
+              let* jsoo = jsoo in
+              Action_builder.of_memo (Version.jsoo_version jsoo)
+            in
+            Command.Args.S
+              (List.map (Config.to_flags ~jsoo_version config) ~f:(fun x ->
+                 Command.Args.A x))))
     ; A "-o"
     ; Target target
     ; spec
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin1.ml b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin1.ml
new file mode 100644
index 00000000000..bf7f3d4d481
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin1.ml
@@ -0,0 +1,6 @@
+let name = "bin1"
+let hello name = print_endline ("Hi " ^ name)
+
+let () = Library1.hello name
+
+let () = hello Library1.name
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin2.ml b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin2.ml
new file mode 100644
index 00000000000..87c52bec613
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin2.ml
@@ -0,0 +1,6 @@
+let name = "bin2"
+let hello name = print_endline ("Hi " ^ name)
+
+let () = Library1.hello name
+
+let () = hello Library1.name
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin3.ml b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin3.ml
new file mode 100644
index 00000000000..d94b8d12e3a
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/bin3.ml
@@ -0,0 +1,6 @@
+let name = "bin3"
+let hello name = print_endline ("Hi " ^ name)
+
+let () = Library1.hello name
+
+let () = hello Library1.name
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/dune b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/dune
new file mode 100644
index 00000000000..318d0199e47
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/bin/dune
@@ -0,0 +1,23 @@
+(executable
+ (name bin1)
+ (modules bin1)
+ (modes js)
+ (libraries library1)
+ (js_of_ocaml
+  (flags (:standard --enable use-js-string))))
+
+(executable
+ (name bin2)
+ (modules bin2)
+ (modes js)
+ (libraries library1)
+ (js_of_ocaml
+  (flags (:standard --disable use-js-string))))
+
+(executable
+ (name bin3)
+ (modules bin3)
+ (modes js)
+ (libraries library1)
+ (js_of_ocaml
+  (flags (:standard --effects=cps))))
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune
new file mode 100644
index 00000000000..1b049a5f23f
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune
@@ -0,0 +1,5 @@
+(env
+ (_
+  (js_of_ocaml
+   (flags (:standard --quiet))
+   (compilation_mode separate))))
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune-project b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune-project
new file mode 100644
index 00000000000..ef5a4287866
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/dune-project
@@ -0,0 +1 @@
+(lang dune 3.0)
\ No newline at end of file
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/dune b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/dune
new file mode 100644
index 00000000000..b049d501c31
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/dune
@@ -0,0 +1,6 @@
+(library
+  (name library1)
+  (js_of_ocaml
+    ;; This will be ignored as the library is compiled once for every effect
+    ;; config and then the version needed by each individual executable is used
+    (flags (:standard --effects=double-translation))))
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/library1.ml b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/library1.ml
new file mode 100644
index 00000000000..70ad25d7d71
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/lib/library1.ml
@@ -0,0 +1,3 @@
+let name = "library1"
+
+let hello name = print_endline ("Hello " ^ name)
diff --git a/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/run.t b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/run.t
new file mode 100644
index 00000000000..c5c7922d8c8
--- /dev/null
+++ b/test/blackbox-tests/test-cases/jsoo/jsoo-config-effects.t/run.t
@@ -0,0 +1,13 @@
+This tests a js_of_ocaml config of linking the same library with different,
+incompatible `--effects` flags
+
+  $ dune build bin/bin1.bc.js bin/bin2.bc.js bin/bin3.bc.js
+  $ node _build/default/bin/bin1.bc.js
+  Hello bin1
+  Hi library1
+  $ node _build/default/bin/bin2.bc.js
+  Hello bin2
+  Hi library1
+  $ node _build/default/bin/bin3.bc.js
+  Hello bin3
+  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 280a783d2ed..a4086af8964 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
@@ -2,11 +2,11 @@ Compilation using jsoo
 
   $ dune build --display short bin/technologic.bc.js @install  2>&1 | \
   > sed s,^\ *$(ocamlc -config-var c_compiler),\ \ C_COMPILER,g
-   js_of_ocaml bin/.technologic.eobjs/jsoo/technologic.bc.runtime.js
       ocamldep bin/.technologic.eobjs/technologic.impl.d
       ocamldep lib/.x.objs/x.impl.d
         ocamlc lib/.x.objs/byte/x__.{cmi,cmo,cmt}
       ocamldep lib/.x.objs/x__Y.impl.d
+   js_of_ocaml bin/.technologic.eobjs/jsoo/technologic.bc.runtime.js
       ocamldep bin/.technologic.eobjs/z.impl.d
       ocamlopt lib/.x.objs/native/x__.{cmx,o}
         ocamlc lib/.x.objs/byte/x__Y.{cmi,cmo,cmt}
diff --git a/test/blackbox-tests/test-cases/wasmoo/no-check-prim.t/run.t b/test/blackbox-tests/test-cases/wasmoo/no-check-prim.t/run.t
index 79999cde7db..04b6dec2de9 100644
--- a/test/blackbox-tests/test-cases/wasmoo/no-check-prim.t/run.t
+++ b/test/blackbox-tests/test-cases/wasmoo/no-check-prim.t/run.t
@@ -2,11 +2,11 @@ Compilation using WasmOO
 
   $ dune build --display short bin/technologic.bc.wasm.js @install  2>&1 | \
   > sed s,^\ *$(ocamlc -config-var c_compiler),\ \ C_COMPILER,g
-  wasm_of_ocaml bin/.technologic.eobjs/jsoo/technologic.bc.runtime.wasma
       ocamldep bin/.technologic.eobjs/dune__exe__Technologic.impl.d
       ocamldep lib/.x.objs/x.impl.d
         ocamlc lib/.x.objs/byte/x__.{cmi,cmo,cmt}
       ocamldep lib/.x.objs/x__Y.impl.d
+  wasm_of_ocaml bin/.technologic.eobjs/jsoo/technologic.bc.runtime.wasma
       ocamldep bin/.technologic.eobjs/dune__exe__Z.impl.d
       ocamlopt lib/.x.objs/native/x__.{cmx,o}
         ocamlc lib/.x.objs/byte/x__Y.{cmi,cmo,cmt}