diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 91d31ab..cf1cc0a 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1772,6 +1772,7 @@
 
 		discount_amount = set_early_payment_discount_loss(pe, doc, valid_discounts, discount_amount)
 		if discount_amount > 0:
+			# Set pending discount amount in deductions
 			pe.set_gain_or_loss(
 				account_details={
 					"account": frappe.get_cached_value("Company", pe.company, "default_discount_account"),
@@ -1780,7 +1781,8 @@
 					"amount": discount_amount * (-1 if payment_type == "Pay" else 1),
 				}
 			)
-			pe.set_difference_amount()
+
+		pe.set_difference_amount()
 
 	return pe