diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 0344e3d..63c5fa9 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1055,64 +1055,76 @@
 				item=self,
 			)
 
-			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)
-
-				if self.book_advance_payments_in_separate_party_account:
-					against_voucher_type = "Payment Entry"
-					against_voucher = self.name
-				else:
-					against_voucher_type = d.reference_doctype
-					against_voucher = d.reference_name
-
-				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": against_voucher_type,
-						"against_voucher": against_voucher,
-						"cost_center": cost_center,
-					}
-				)
-				gl_entries.append(gle)
-
 			dr_or_cr = "credit" if self.payment_type == "Receive" else "debit"
-			if self.unallocated_amount:
-				exchange_rate = self.get_exchange_rate()
-				base_unallocated_amount = self.unallocated_amount * exchange_rate
+			if self.book_advance_payments_in_separate_party_account:
+				if self.payment_type == "Receive":
+					amount = self.base_paid_amount
+				else:
+					amount = self.base_received_amount
 
 				gle = party_gl_dict.copy()
 				gle.update(
 					{
-						dr_or_cr + "_in_account_currency": self.unallocated_amount,
-						dr_or_cr: base_unallocated_amount,
+						dr_or_cr: amount,
+						# TODO: handle multi currency payments
+						dr_or_cr + "_in_account_currency": amount,
+						"against_voucher_type": "Payment Entry",
+						"against_voucher": self.name,
+						"cost_center": self.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:
+					exchange_rate = self.get_exchange_rate()
+					base_unallocated_amount = self.unallocated_amount * exchange_rate
+
+					gle = party_gl_dict.copy()
+					gle.update(
+						{
+							dr_or_cr + "_in_account_currency": self.unallocated_amount,
+							dr_or_cr: base_unallocated_amount,
+						}
+					)
+
+					gl_entries.append(gle)
 
 	def make_advance_gl_entries(self, against_voucher_type=None, against_voucher=None, cancel=0):
 		if self.book_advance_payments_in_separate_party_account:
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index d133307..e2632d3 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -499,7 +499,7 @@
 
 		if voucher_type == "Payment Entry" and doc.book_advance_payments_in_separate_party_account:
 			# both ledgers must be posted to for `Advance as Liability`
-			doc.make_gl_entries()
+			doc.make_advance_gl_entries()
 		else:
 			gl_map = doc.build_gl_map()
 			create_payment_ledger_entry(gl_map, update_outstanding="No", cancel=0, adv_adj=1)