diff --git a/frappe/desk/page/setup_wizard/setup_wizard.py b/frappe/desk/page/setup_wizard/setup_wizard.py
index cf8f5f502b..a18d4df9c4 100755
--- a/frappe/desk/page/setup_wizard/setup_wizard.py
+++ b/frappe/desk/page/setup_wizard/setup_wizard.py
@@ -389,7 +389,7 @@ def make_records(records, debug=False):
 			# pass DuplicateEntryError and continue
 			if e.args and e.args[0]==doc.doctype and e.args[1]==doc.name:
 				# make sure DuplicateEntryError is for the exact same doc and not a related doc
-				pass
+				frappe.clear_messages()
 			else:
 				raise