diff --git a/Makefile b/Makefile
index 99e742d6..2c7bb808 100644
--- a/Makefile
+++ b/Makefile
@@ -98,8 +98,16 @@ distclean: clean
 	@@rm -rf test/qunit src/sizzle
 
 # change pointers for submodules and update them to what is specified in jQuery
+# --merge  doesn't work when doing an initial clone, thus test if we have non-existing
+#  submodules, then do an real update
 update_submodules:
-	@@if [ -d .git ]; then git submodule update --init --recursive --merge; fi
+	@@if [ -d .git ]; then \
+		if git submodule status | grep -q -E '^-'; then \
+			git submodule update --init --recursive; \
+		else \
+			git submodule update --init --recursive --merge; \
+		fi; \
+	fi;
 
 # update the submodules to the latest at the most logical branch
 pull_submodules: