diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index b283c8fcb67..09bd7d2cc88 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -79,6 +79,7 @@ class PaymentReconciliation(Document):
 				`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}
 			group by voucher_type, voucher_no
 		""".format(**{
diff --git a/erpnext/accounts/doctype/payment_tool/payment_tool.py b/erpnext/accounts/doctype/payment_tool/payment_tool.py
index 924fd1e1c6d..eedf69fe5db 100644
--- a/erpnext/accounts/doctype/payment_tool/payment_tool.py
+++ b/erpnext/accounts/doctype/payment_tool/payment_tool.py
@@ -58,7 +58,7 @@ def get_outstanding_vouchers(args):
 		frappe.throw(_("No permission to use Payment Tool"), frappe.PermissionError)
 
 	args = json.loads(args)
-	
+
 	party_account_currency = frappe.db.get_value("Account", args.get("party_account"), "account_currency")
 	company_currency = frappe.db.get_value("Company", args.get("company"), "default_currency")
 
@@ -71,18 +71,18 @@ def get_outstanding_vouchers(args):
 
 	# Get all outstanding sales /purchase invoices
 	outstanding_invoices = get_outstanding_invoices(amount_query, args.get("party_account"),
-		args.get("party_type"), args.get("party"))
+		args.get("party_type"), args.get("party"), with_journal_entry=False)
 
 	# 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"), 
+	orders_to_be_billed = get_orders_to_be_billed(args.get("party_type"), args.get("party"),
 		party_account_currency, company_currency)
 	return outstanding_invoices + orders_to_be_billed
 
 def get_orders_to_be_billed(party_type, party, party_account_currency, company_currency):
 	voucher_type = 'Sales Order' if party_type == "Customer" else 'Purchase Order'
-	
+
 	ref_field = "base_grand_total" if party_account_currency == company_currency else "grand_total"
-	
+
 	orders = frappe.db.sql("""
 		select
 			name as voucher_no,
@@ -115,7 +115,7 @@ def get_against_voucher_amount(against_voucher_type, against_voucher_no, party_a
 	party_account_currency = frappe.db.get_value("Account", party_account, "account_currency")
 	company_currency = frappe.db.get_value("Company", company, "default_currency")
 	ref_field = "base_grand_total" if party_account_currency == company_currency else "grand_total"
-	
+
 	if against_voucher_type in ["Sales Order", "Purchase Order"]:
 		select_cond = "{0} as total_amount, ifnull({0}, 0) - ifnull(advance_paid, 0) as outstanding_amount"\
 			.format(ref_field)
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 89ff6cff15d..e1bb9ead333 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -100,7 +100,7 @@ def get_balance_on(account=None, date=None, party_type=None, party=None, in_acco
 	if party_type and party:
 		cond.append("""gle.party_type = "%s" and gle.party = "%s" """ %
 			(party_type.replace('"', '\\"'), party.replace('"', '\\"')))
-			
+
 	if account or (party_type and party):
 		if in_account_currency:
 			select_field = "sum(ifnull(debit_in_account_currency, 0)) - sum(ifnull(credit_in_account_currency, 0))"
@@ -202,7 +202,7 @@ def update_against_doc(d, jv_obj):
 			select cost_center, balance, against_account, is_advance, account_type, exchange_rate
 			from `tabJournal Entry Account` where name = %s
 		""", d['voucher_detail_no'], as_dict=True)
-		
+
 		# new entry with balance amount
 		ch = jv_obj.append("accounts")
 		ch.account = d['account']
@@ -392,7 +392,7 @@ def get_stock_rbnb_difference(posting_date, company):
 	# Amount should be credited
 	return flt(stock_rbnb) + flt(sys_bal)
 
-def get_outstanding_invoices(amount_query, account, party_type, party):
+def get_outstanding_invoices(amount_query, account, party_type, party, with_journal_entry=True):
 	all_outstanding_vouchers = []
 	outstanding_voucher_list = frappe.db.sql("""
 		select
@@ -420,6 +420,9 @@ def get_outstanding_invoices(amount_query, account, party_type, party):
 		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({