diff --git a/erpnext/controllers/stock_controller.py b/erpnext/controllers/stock_controller.py
index 2f275bb3c91..8cad82c3e25 100644
--- a/erpnext/controllers/stock_controller.py
+++ b/erpnext/controllers/stock_controller.py
@@ -242,10 +242,11 @@ class StockController(AccountsController):
 					_(self.doctype), self.name, item.get("item_code")))
 
 	def delete_auto_created_batches(self):
+		from erpnext.stock.doctype.serial_no.serial_no import get_serial_nos
 		for d in self.items:
 			if not d.batch_no: continue
 
-			serial_nos = [sr.name for sr in frappe.get_all("Serial No", {'batch_no': d.batch_no})]
+			serial_nos = get_serial_nos(d.serial_no)
 			if serial_nos:
 				frappe.db.set_value("Serial No", { 'name': ['in', serial_nos] }, "batch_no", None)
 
diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index 0dc87767dde..00dc7725039 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -45,6 +45,7 @@ class StockReconciliation(StockController):
 	def on_cancel(self):
 		self.delete_and_repost_sle()
 		self.make_gl_entries_on_cancel()
+		self.delete_auto_created_batches()
 
 	def remove_items_with_no_change(self):
 		"""Remove items if qty or rate is not changed"""