diff --git a/bootstrap b/bootstrap
index 142509944..d862b5652 100755
--- a/bootstrap
+++ b/bootstrap
@@ -11,6 +11,7 @@ if ! git --version >/dev/null; then
 fi
 
 git submodule update --init
+rm -rf configure
 cp build-system/taler-build-scripts/configure ./configure
 # Try making the configure script read-only to prevent
 # accidental changes in the wrong place.