diff --git a/meta/classes/autotools.bbclass b/meta/classes/autotools.bbclass
index b97d74b..6539df9 100644
--- a/meta/classes/autotools.bbclass
+++ b/meta/classes/autotools.bbclass
@@ -93,10 +93,15 @@ CONFIGURESTAMPFILE = "${WORKDIR}/configure.sstate"
 
 autotools_preconfigure() {
 	if [ -n "${CONFIGURESTAMPFILE}" -a -e "${CONFIGURESTAMPFILE}" ]; then
-		if [ "`cat ${CONFIGURESTAMPFILE}`" != "${BB_TASKHASH}" -a "${S}" != "${B}" ]; then
-			echo "Previously configured separate build directory detected, cleaning ${B}"
-			rm -rf ${B}
-			mkdir ${B}
+		if [ "`cat ${CONFIGURESTAMPFILE}`" != "${BB_TASKHASH}" ]; then
+			if [ "${S}" != "${B}" ]; then
+				echo "Previously configured separate build directory detected, cleaning ${B}"
+				rm -rf ${B}
+				mkdir ${B}
+			else
+				echo "Previously configured source directory detected, cleaning ${S}"
+				( oe_runmake clean ) || true
+			fi
 		fi
 	fi
 }