diff --git a/Tools/check_submodules.sh b/Tools/check_submodules.sh
index fb180ef47e..4b8789b288 100755
--- a/Tools/check_submodules.sh
+++ b/Tools/check_submodules.sh
@@ -1,5 +1,12 @@
 #!/bin/sh
 
+[ -n "$NUTTX_SRC" ] && {
+    # NUTTX_SRC is set, meaning user is overriding the NuttX tree to use. Don't 
+    # use submodules to pull an alternatiie tree
+    echo "Skipping submodules as NUTTX_SRC is set to $NUTTX_SRC"
+    exit 0
+}
+
 if [ -d NuttX/nuttx ];
 	then
 	STATUSRETVAL=$(git status --porcelain | grep -i "NuttX")