diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index a4319521e36..55b314c98fd 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -60,6 +60,7 @@ class PaymentEntry(AccountsController):
 	def validate(self):
 		self.setup_party_account_field()
 		self.set_missing_values()
+		self.set_missing_ref_details()
 		self.validate_payment_type()
 		self.validate_party_details()
 		self.set_exchange_rate()
@@ -219,8 +220,6 @@ class PaymentEntry(AccountsController):
 			else self.paid_to_account_currency
 		)
 
-		self.set_missing_ref_details()
-
 	def set_missing_ref_details(self, force=False):
 		for d in self.get("references"):
 			if d.allocated_amount:
@@ -1811,6 +1810,7 @@ def get_payment_entry(
 
 	pe.setup_party_account_field()
 	pe.set_missing_values()
+	pe.set_missing_ref_details()
 
 	update_accounting_dimensions(pe, doc)
 
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index 4ab0d56f681..7fd6242b9c6 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -632,6 +632,12 @@ def update_reference_in_payment_entry(d, payment_entry, do_not_save=False):
 
 		payment_entry.set_gain_or_loss(account_details=account_details)
 
+	payment_entry.flags.ignore_validate_update_after_submit = True
+	payment_entry.setup_party_account_field()
+	payment_entry.set_missing_values()
+	payment_entry.set_missing_ref_details()
+	payment_entry.set_amounts()
+
 	if not do_not_save:
 		payment_entry.save(ignore_permissions=True)