diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 16ca88bd810c..be4152112663 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -61,6 +61,7 @@ def on_cancel(self):
 		self.make_sle_on_cancel()
 		self.make_gl_entries_on_cancel()
 		self.repost_future_sle_and_gle()
+		self.delete_auto_created_batches()
 
 	def remove_items_with_no_change(self):
 		"""Remove items if qty or rate is not changed"""