diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index efd6d6cfe..72b8554fa 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -123,7 +123,7 @@ jobs:
 
       - name: Pin dune
         run: |
-          opam pin add -n dune.3.13 https://github.com/ocaml-wasm/dune.git#wasm
+          opam pin add -n dune.3.13 https://github.com/ocaml-wasm/dune.git#wasm-separate-compilation
 
       - name: Pin wasm_of_ocaml
         working-directory: ./wasm_of_ocaml
diff --git a/dune b/dune
index 332a72301..692e05102 100644
--- a/dune
+++ b/dune
@@ -12,10 +12,12 @@
  (wasm
   (binaries (tools/node_wrapper.sh as node))
   (js_of_ocaml
+   (compilation_mode separate)
    (targets wasm)))
  (wasm-effects
   (binaries (tools/node_wrapper.sh as node))
   (js_of_ocaml
+   (compilation_mode separate)
    (flags
     (:standard --enable effects))
    (targets wasm)))
diff --git a/tools/ci_setup.ml b/tools/ci_setup.ml
index fb162b2be..c37ae4918 100644
--- a/tools/ci_setup.ml
+++ b/tools/ci_setup.ml
@@ -18,7 +18,7 @@ let omitted_others = StringSet.of_list [ "cohttp-async"; "cohttp"; "uri"; "uri-s
 
 let omitted_js = StringSet.of_list [ "sexplib0" ]
 
-let do_not_pin = StringSet.of_list [ "wasocaml"; "wasm_of_ocaml" ]
+let do_not_pin = StringSet.of_list [ "wasocaml"; "wasm_of_ocaml"; "dune" ]
 
 let do_pin = StringSet.of_list [ "base"; "ppx_expect"; "ppx_inline_test"; "time_now" ]