diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index 2f8b634664..791b03a0d7 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -99,6 +99,7 @@ class PaymentReconciliation(Document):
 				and `tabGL Entry`.against_voucher_type = %(voucher_type)s
 				and `tab{doc}`.docstatus = 1 and `tabGL Entry`.party = %(party)s
 				and `tabGL Entry`.party_type = %(party_type)s and `tabGL Entry`.account = %(account)s
+				and `tabGL Entry`.is_cancelled = 0
 			GROUP BY `tab{doc}`.name
 			Having
 				amount > 0