diff --git a/scripts/setup-app-layer.py b/scripts/setup-app-layer.py
index eb1e601a72..f20b4d9884 100755
--- a/scripts/setup-app-layer.py
+++ b/scripts/setup-app-layer.py
@@ -341,6 +341,13 @@ def main():
         parser = args.parser
         logger = args.logger
 
+    # Make sure we are in the correct directory.
+    if os.path.exists("./suricata.c"):
+        os.chdir("..")
+    elif not os.path.exists("./src/suricata.c"):
+        raise SetupError(
+            "this does not appear to be a Suricata source directory.")
+
     if parser:
         if proto_exists(proto):
             raise SetupError("protocol already exists: %s" % (proto))