diff --git a/erpnext/accounts/doctype/bank_reconciliation_tool/bank_reconciliation_tool.py b/erpnext/accounts/doctype/bank_reconciliation_tool/bank_reconciliation_tool.py
index e512d98cd88..2fd49c962f7 100644
--- a/erpnext/accounts/doctype/bank_reconciliation_tool/bank_reconciliation_tool.py
+++ b/erpnext/accounts/doctype/bank_reconciliation_tool/bank_reconciliation_tool.py
@@ -345,7 +345,9 @@ def create_payment_entry_bts(
 	pe.mode_of_payment = mode_of_payment
 	pe.project = project
 	pe.cost_center = cost_center
-	pe.bank_account = company_bank_account
+
+	if company_bank_account:
+		pe.bank_account = company_bank_account
 
 	pe.validate()
 
diff --git a/erpnext/public/js/bank_reconciliation_tool/dialog_manager.js b/erpnext/public/js/bank_reconciliation_tool/dialog_manager.js
index 9879ede4ef3..16d4e9971d8 100644
--- a/erpnext/public/js/bank_reconciliation_tool/dialog_manager.js
+++ b/erpnext/public/js/bank_reconciliation_tool/dialog_manager.js
@@ -526,7 +526,7 @@ erpnext.accounts.bank_reconciliation.DialogManager = class DialogManager {
 				mode_of_payment: values.mode_of_payment,
 				project: values.project,
 				cost_center: values.cost_center,
-				company_bank_account: values?.company_bank_account || this?.bank_account,
+				company_bank_account: values?.bank_account || this?.bank_account,
 			},
 			callback: (response) => {
 				const alert_string = __("Bank Transaction {0} added as Payment Entry", [
@@ -598,7 +598,7 @@ erpnext.accounts.bank_reconciliation.DialogManager = class DialogManager {
 					project: values.project,
 					cost_center: values.cost_center,
 					allow_edit: true,
-					company_bank_account: values?.company_bank_account || this?.bank_account,
+					company_bank_account: values?.bank_account || this?.bank_account,
 				},
 				callback: (r) => {
 					const doc = frappe.model.sync(r.message);