diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 26c88536e45..453a7b1202d 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1131,73 +1131,49 @@ class PaymentEntry(AccountsController):
 			)
 
 			dr_or_cr = "credit" if self.payment_type == "Receive" else "debit"
-			if self.book_advance_payments_in_separate_party_account:
+
+			for d in self.get("references"):
+				# re-defining dr_or_cr for every reference in order to avoid the last value affecting calculation of reverse
+				dr_or_cr = "credit" if self.payment_type == "Receive" else "debit"
+				cost_center = self.cost_center
+				if d.reference_doctype == "Sales Invoice" and not cost_center:
+					cost_center = frappe.db.get_value(d.reference_doctype, d.reference_name, "cost_center")
+
 				gle = party_gl_dict.copy()
 
-				if self.payment_type == "Receive":
-					amount = self.base_paid_amount
-				else:
-					amount = self.base_received_amount
+				allocated_amount_in_company_currency = self.calculate_base_allocated_amount_for_reference(d)
+				reverse_dr_or_cr = 0
+
+				if d.reference_doctype in ["Sales Invoice", "Purchase Invoice"]:
+					is_return = frappe.db.get_value(d.reference_doctype, d.reference_name, "is_return")
+					payable_party_types = get_party_types_from_account_type("Payable")
+					receivable_party_types = get_party_types_from_account_type("Receivable")
+					if (
+						is_return
+						and self.party_type in receivable_party_types
+						and (self.payment_type == "Pay")
+					):
+						reverse_dr_or_cr = 1
+					elif (
+						is_return
+						and self.party_type in payable_party_types
+						and (self.payment_type == "Receive")
+					):
+						reverse_dr_or_cr = 1
+
+					if is_return and not reverse_dr_or_cr:
+						dr_or_cr = "debit" if dr_or_cr == "credit" else "credit"
 
-				exchange_rate = self.get_exchange_rate()
-				amount_in_account_currency = amount * exchange_rate
 				gle.update(
 					{
-						dr_or_cr: amount,
-						dr_or_cr + "_in_account_currency": amount_in_account_currency,
-						"against_voucher_type": "Payment Entry",
-						"against_voucher": self.name,
-						"cost_center": self.cost_center,
+						dr_or_cr: abs(allocated_amount_in_company_currency),
+						dr_or_cr + "_in_account_currency": abs(d.allocated_amount),
+						"against_voucher_type": d.reference_doctype,
+						"against_voucher": d.reference_name,
+						"cost_center": cost_center,
 					}
 				)
 				gl_entries.append(gle)
-			else:
-				for d in self.get("references"):
-					# re-defining dr_or_cr for every reference in order to avoid the last value affecting calculation of reverse
-					dr_or_cr = "credit" if self.payment_type == "Receive" else "debit"
-					cost_center = self.cost_center
-					if d.reference_doctype == "Sales Invoice" and not cost_center:
-						cost_center = frappe.db.get_value(
-							d.reference_doctype, d.reference_name, "cost_center"
-						)
-
-					gle = party_gl_dict.copy()
-
-					allocated_amount_in_company_currency = self.calculate_base_allocated_amount_for_reference(
-						d
-					)
-					reverse_dr_or_cr = 0
-
-					if d.reference_doctype in ["Sales Invoice", "Purchase Invoice"]:
-						is_return = frappe.db.get_value(d.reference_doctype, d.reference_name, "is_return")
-						payable_party_types = get_party_types_from_account_type("Payable")
-						receivable_party_types = get_party_types_from_account_type("Receivable")
-						if (
-							is_return
-							and self.party_type in receivable_party_types
-							and (self.payment_type == "Pay")
-						):
-							reverse_dr_or_cr = 1
-						elif (
-							is_return
-							and self.party_type in payable_party_types
-							and (self.payment_type == "Receive")
-						):
-							reverse_dr_or_cr = 1
-
-						if is_return and not reverse_dr_or_cr:
-							dr_or_cr = "debit" if dr_or_cr == "credit" else "credit"
-
-					gle.update(
-						{
-							dr_or_cr: abs(allocated_amount_in_company_currency),
-							dr_or_cr + "_in_account_currency": abs(d.allocated_amount),
-							"against_voucher_type": d.reference_doctype,
-							"against_voucher": d.reference_name,
-							"cost_center": cost_center,
-						}
-					)
-					gl_entries.append(gle)
 
 				if self.unallocated_amount:
 					dr_or_cr = "credit" if self.payment_type == "Receive" else "debit"
@@ -1212,6 +1188,13 @@ class PaymentEntry(AccountsController):
 						}
 					)
 
+					if self.book_advance_payments_in_separate_party_account:
+						gle.update(
+							{
+								"against_voucher_type": "Payment Entry",
+								"against_voucher": self.name,
+							}
+						)
 					gl_entries.append(gle)
 
 	def make_advance_gl_entries(