diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index b8ba5347510..0248cdfbcf0 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -3,7 +3,7 @@
 
 
 import frappe
-from frappe import _, msgprint
+from frappe import _, bold, msgprint
 from frappe.utils import cint, cstr, flt
 
 import erpnext
@@ -88,7 +88,7 @@ class StockReconciliation(StockController):
 
 				if item_dict.get("serial_nos"):
 					item.current_serial_no = item_dict.get("serial_nos")
-					if self.purpose == "Stock Reconciliation" and not item.serial_no:
+					if self.purpose == "Stock Reconciliation" and not item.serial_no and item.qty:
 						item.serial_no = item.current_serial_no
 
 				item.current_qty = item_dict.get("qty")
@@ -139,6 +139,14 @@ class StockReconciliation(StockController):
 
 			self.validate_item(row.item_code, row)
 
+			if row.serial_no and not row.qty:
+				self.validation_messages.append(
+					_get_msg(
+						row_num,
+						f"Quantity should not be zero for the {bold(row.item_code)} since serial nos are specified",
+					)
+				)
+
 			# validate warehouse
 			if not frappe.db.get_value("Warehouse", row.warehouse):
 				self.validation_messages.append(_get_msg(row_num, _("Warehouse not found in the system")))