diff --git a/Makefile b/Makefile
index 79ec35affce..00e8ad1d7e4 100644
--- a/Makefile
+++ b/Makefile
@@ -6,7 +6,7 @@ all: opam opam-installer
 	@
 
 ifeq ($(DUNE),)
-  DUNE_EXE = src_ext/dune-local/_build/install/default/bin/dune$(EXE)
+  DUNE_EXE = src_ext/dune-local/_build_bootstrap/install/default/bin/dune$(EXE)
   ifeq ($(shell command -v cygpath 2>/dev/null),)
     DUNE := $(DUNE_EXE)
   else
@@ -26,7 +26,7 @@ JBUILDER_ARGS ?=
 DUNE_ARGS ?= $(JBUILDER_ARGS)
 DUNE_PROFILE ?= release
 
-src_ext/dune-local/_build/install/default/bin/dune$(EXE): src_ext/dune-local.stamp
+src_ext/dune-local/_build_bootstrap/install/default/bin/dune$(EXE): src_ext/dune-local.stamp
 	cd src_ext/dune-local && ocaml bootstrap.ml && ./boot.exe --release
 
 src_ext/dune-local.stamp:
diff --git a/doc/Makefile b/doc/Makefile
index 9f00bfd597c..033a42fd361 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,7 +1,7 @@
 -include ../Makefile.config
 
 ifeq ($(DUNE),)
-  DUNE_EXE = ../src_ext/dune-local/_build/install/default/bin/dune$(EXE)
+  DUNE_EXE = ../src_ext/dune-local/_build_bootstrap/install/default/bin/dune$(EXE)
   ifeq ($(shell command -v cygpath 2>/dev/null),)
     DUNE := $(DUNE_EXE)
   else
diff --git a/src_ext/Makefile b/src_ext/Makefile
index cc0a0d612ec..b83b9029b8c 100644
--- a/src_ext/Makefile
+++ b/src_ext/Makefile
@@ -79,7 +79,7 @@ reset-lib-pkg:
 	@rm -rf ../bootstrap/ocaml/lib/ocaml/site-lib ../bootstrap/ocaml/etc *.pkgbuild
 
 ifeq ($(DUNE),)
-DUNE_DEP=dune-local/_build/install/default/bin/dune$(EXE)
+DUNE_DEP=dune-local/_build_bootstrap/install/default/bin/dune$(EXE)
 DUNE_CLONE=dune-local.stamp
 ifeq ($(shell command -v cygpath 2>/dev/null),)
 DUNE:=$(DUNE_DEP)
@@ -91,7 +91,7 @@ DUNE_DEP=
 DUNE_CLONE=
 endif
 
-dune-local/_build/install/default/bin/dune$(EXE): $(DUNE_CLONE)
+dune-local/_build_bootstrap/install/default/bin/dune$(EXE): $(DUNE_CLONE)
 	cd dune-local && ocaml bootstrap.ml && ./boot.exe --release
 
 build-pkg: clone-pkg $(PKG_EXTS:=.pkgbuild)
diff --git a/src_ext/Makefile.packages b/src_ext/Makefile.packages
index 087e42d35da..84a392286b5 100644
--- a/src_ext/Makefile.packages
+++ b/src_ext/Makefile.packages
@@ -95,7 +95,7 @@ dose3-pkg-build:
 dune-local-pkg-build:
 	ocaml bootstrap.ml
 	./boot.exe --release
-	cp _build/default/bin/main_dune.exe $(OCAMLBIN)/dune$(EXT_EXE)
+	cp _build_bootstrap/default/bin/main_dune.exe $(OCAMLBIN)/dune$(EXT_EXE)
 
 mccs-pkg-build:
 	dune build @install --root=.
diff --git a/src_ext/Makefile.sources b/src_ext/Makefile.sources
index f8ce6c592e1..07a6038aed9 100644
--- a/src_ext/Makefile.sources
+++ b/src_ext/Makefile.sources
@@ -48,8 +48,8 @@ MD5_result = 4beebefd41f7f899b6eeba7414e7ae01
 
 $(call PKG_SAME,result)
 
-URL_dune-local = https://github.com/ocaml/dune/releases/download/1.2.1/dune-1.2.1.tbz
-MD5_dune-local = f96bdf1a893a2178c2ad9c388439bd18
+URL_dune-local = https://github.com/ocaml/dune/releases/download/1.6.3/dune-1.6.3.tbz
+MD5_dune-local = 1212a36547d25269675d767c38fecf5f
 
 $(call PKG_SAME,dune-local)