diff --git a/bootstrap b/bootstrap
index 3b60fc6e5..ad5e7bdd2 100755
--- a/bootstrap
+++ b/bootstrap
@@ -39,5 +39,12 @@ else
     git submodule update
 fi
 
+if [ -x src/jtag/drivers/libjaylink/autogen.sh ]; then
+    (
+    cd src/jtag/drivers/libjaylink
+    ./autogen.sh
+    )
+fi
+
 echo "Bootstrap complete. Quick build instructions:"
 echo "./configure ...."
diff --git a/configure.ac b/configure.ac
index 1fcafe064..52b2e964f 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1186,7 +1186,6 @@ AM_CONDITIONAL([HLADAPTER], [test $enable_stlink != no -o $enable_ti_icdi != no]
 if test $enable_jlink != no; then
   if test $use_internal_libjaylink = yes; then
     if test -f "$srcdir/src/jtag/drivers/libjaylink/configure.ac"; then
-      ( cd $srcdir/src/jtag/drivers/libjaylink/ && ./autogen.sh )
       AX_CONFIG_SUBDIR_OPTION([src/jtag/drivers/libjaylink],
 		[--enable-subproject-build])
     else