diff --git a/Makefile b/Makefile
index 79798fea4..c3b2c4e01 100644
--- a/Makefile
+++ b/Makefile
@@ -109,8 +109,13 @@ ifeq (1, $(USE_SYS_DUNE_HACK))
 	opam repo add upstream "git+https://github.com/ocaml/opam-repository.git" --on-switch=$(CONFIG_SWITCH_NAME) --rank 2
 	opam install --switch=$(CONFIG_SWITCH_NAME) --yes ocamlfind
 	opam install --switch=$(CONFIG_SWITCH_NAME) --yes "dune.$(SANDMARK_DUNE_VERSION)" "dune-configurator.$(SANDMARK_DUNE_VERSION)"
-	# Pin the version so it doesn't change when installing packages
-	opam pin add --switch=$(CONFIG_SWITCH_NAME) --yes -n dune "$(SANDMARK_DUNE_VERSION)"
+	@{ case "$*" in \
+		5.3.*) \
+			echo "Pinning dune to fixed version to work around binary and native compiler options split"; \
+			opam pin add --yes --switch $* dune."$(SANDMARK_DUNE_VERSION)" https://github.com/punchagan/dune.git#fix-compiler-opts;; \
+		*) \
+			opam pin add --switch=$(CONFIG_SWITCH_NAME) --yes -n dune "$(SANDMARK_DUNE_VERSION)" ;; \
+	esac };
 endif
 
 ocamls=$(wildcard ocaml-versions/*.json)