diff --git a/frappe/website/doctype/portal_settings/portal_settings.py b/frappe/website/doctype/portal_settings/portal_settings.py
index 78c2b2d20d..b983548062 100644
--- a/frappe/website/doctype/portal_settings/portal_settings.py
+++ b/frappe/website/doctype/portal_settings/portal_settings.py
@@ -49,6 +49,7 @@ class PortalSettings(Document):
 				dirty = True
 
 		if dirty:
+			self.remove_deleted_doctype_items()
 			self.save()
 
 	def on_update(self):
@@ -65,3 +66,9 @@ class PortalSettings(Document):
 
 		# clears role based home pages
 		frappe.clear_cache()
+
+	def remove_deleted_doctype_items(self):
+		existing_doctypes = set(frappe.get_list("DocType", pluck="name"))
+		for menu_item in list(self.get("menu")):
+			if menu_item.reference_doctype not in existing_doctypes:
+				self.remove(menu_item)