diff --git a/configure.ml b/boot/configure.ml
similarity index 100%
rename from configure.ml
rename to boot/configure.ml
diff --git a/boot/dune b/boot/dune
index 3e3b39be382..3f7f6065608 100644
--- a/boot/dune
+++ b/boot/dune
@@ -9,6 +9,7 @@
 
 (executable
  (name duneboot)
+ (modules :standard \ configure)
  (libraries unix))
 
 ;; For unused value warnings. We don't write a plain empty
diff --git a/configure b/configure
index eb093a5536f..efc50aa3f9b 100755
--- a/configure
+++ b/configure
@@ -1,2 +1,2 @@
 #!/bin/sh
-exec ocaml configure.ml "$@"
+exec ocaml boot/configure.ml "$@"
diff --git a/src/dune_rules/dune b/src/dune_rules/dune
index aa7022e557a..8f3dd92e80d 100644
--- a/src/dune_rules/dune
+++ b/src/dune_rules/dune
@@ -55,11 +55,12 @@
  (mode promote)
  (alias runtest)
  (targets setup.defaults.ml)
- (deps %{project_root}/configure.ml)
+ (deps
+  (:configure %{project_root}/boot/configure.ml))
  (action
   (chdir
    %{project_root}
    (setenv
     DUNE_CONFIGURE_OUTPUT
     "src/dune_rules/setup.defaults.ml"
-    (run %{ocaml} configure.ml)))))
+    (run %{ocaml} %{configure})))))