diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index 09bd7d2..743df37 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -70,7 +70,7 @@
 		non_reconciled_invoices = []
 		dr_or_cr = "debit" if self.party_type == "Customer" else "credit"
 		cond = self.check_condition(dr_or_cr)
-
+		
 		invoice_list = frappe.db.sql("""
 			select
 				voucher_no, voucher_type, posting_date,
@@ -79,8 +79,12 @@
 				`tabGL Entry`
 			where
 				party_type = %(party_type)s and party = %(party)s
-				and voucher_type != "Journal Entry"
 				and account = %(account)s and {dr_or_cr} > 0 {cond}
+				and (CASE
+					WHEN voucher_type = 'Journal Entry'
+					THEN ifnull(against_voucher, '') = ''
+					ELSE 1=1
+				END)
 			group by voucher_type, voucher_no
 		""".format(**{
 			"cond": cond,
diff --git a/erpnext/accounts/doctype/payment_tool/payment_tool.py b/erpnext/accounts/doctype/payment_tool/payment_tool.py
index eedf69f..b02214c 100644
--- a/erpnext/accounts/doctype/payment_tool/payment_tool.py
+++ b/erpnext/accounts/doctype/payment_tool/payment_tool.py
@@ -71,7 +71,7 @@
 
 	# Get all outstanding sales /purchase invoices
 	outstanding_invoices = get_outstanding_invoices(amount_query, args.get("party_account"),
-		args.get("party_type"), args.get("party"), with_journal_entry=False)
+		args.get("party_type"), args.get("party"))
 
 	# Get all SO / PO which are not fully billed or aginst which full advance not paid
 	orders_to_be_billed = get_orders_to_be_billed(args.get("party_type"), args.get("party"),
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 04084ed..645c91c 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -397,7 +397,7 @@
 	# Amount should be credited
 	return flt(stock_rbnb) + flt(sys_bal)
 
-def get_outstanding_invoices(amount_query, account, party_type, party, with_journal_entry=True):
+def get_outstanding_invoices(amount_query, account, party_type, party):
 	all_outstanding_vouchers = []
 	outstanding_voucher_list = frappe.db.sql("""
 		select
@@ -407,6 +407,11 @@
 			`tabGL Entry`
 		where
 			account = %s and party_type=%s and party=%s and {amount_query} > 0
+			and (CASE
+					WHEN voucher_type = 'Journal Entry'
+					THEN ifnull(against_voucher, '') = ''
+					ELSE 1=1
+				END)
 		group by voucher_type, voucher_no
 		""".format(amount_query = amount_query), (account, party_type, party), as_dict = True)
 
@@ -425,9 +430,6 @@
 		payment_amount = -1*payment_amount[0][0] if payment_amount else 0
 		precision = frappe.get_precision("Sales Invoice", "outstanding_amount")
 
-		if not with_journal_entry and d.voucher_type=="Journal Entry":
-			continue
-
 		if d.invoice_amount > payment_amount:
 
 			all_outstanding_vouchers.append({