diff --git a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
index d1b81aa2ebe..59208725e7d 100644
--- a/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
+++ b/erpnext/stock/doctype/stock_reconciliation/stock_reconciliation.py
@@ -748,12 +748,12 @@ def get_items(warehouse, posting_date, posting_time, company, item_code=None, ig
 	itemwise_batch_data = get_itemwise_batch(warehouse, posting_date, company, item_code)
 
 	for d in items:
-		if d.item_code in itemwise_batch_data:
+		if (d.item_code, d.warehouse) in itemwise_batch_data:
 			valuation_rate = get_stock_balance(
 				d.item_code, d.warehouse, posting_date, posting_time, with_valuation_rate=True
 			)[1]
 
-			for row in itemwise_batch_data.get(d.item_code):
+			for row in itemwise_batch_data.get((d.item_code, d.warehouse)):
 				if ignore_empty_stock and not row.qty:
 					continue
 
@@ -885,7 +885,7 @@ def get_itemwise_batch(warehouse, posting_date, company, item_code=None):
 	columns, data = execute(filters)
 
 	for row in data:
-		itemwise_batch_data.setdefault(row[0], []).append(
+		itemwise_batch_data.setdefault((row[0], row[3]), []).append(
 			frappe._dict(
 				{
 					"item_code": row[0],