diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index df9aef69bd05b5ca2ca9a5337a70e3e802d6d861..fcfebb3007435b74f6f987244ed422840c539058 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1721,6 +1721,27 @@ class PaymentEntry(AccountsController):
 		return current_tax_fraction
 
 
+	def add_payment_gateway_fees(self, account, cost_center, fees):
+		self.add_deductions(account, cost_center, fees)
+
+	def add_payment_gateway_taxes(self, account, cost_center, taxes):
+		self.add_deductions(account, cost_center, taxes)
+
+	def add_deductions(self, account, cost_center, amount):
+		self.append(
+			"deductions",
+			{
+				"account": account,
+				"cost_center": cost_center,
+				"amount": amount,
+			},
+		)
+
+	def deduct_fees_from_paid_amount(self, fees):
+		self.paid_amount = flt(self.paid_amount) - fees
+		self.received_amount = flt(self.received_amount) - fees
+
+
 def validate_inclusive_tax(tax, doc):
 	def _on_previous_row_error(row_range):
 		throw(
diff --git a/erpnext/accounts/page/bank_reconciliation/stancer_reconciliation.py b/erpnext/accounts/page/bank_reconciliation/stancer_reconciliation.py
index 361440a02b76b4b6d69b71315e19f08b662242c3..34a3bffcd8058dda60e1929931878ebbd6cdc857 100644
--- a/erpnext/accounts/page/bank_reconciliation/stancer_reconciliation.py
+++ b/erpnext/accounts/page/bank_reconciliation/stancer_reconciliation.py
@@ -3,12 +3,19 @@
 
 import re
 
+from typing import TYPE_CHECKING
+
+
 import frappe
 from payments.payment_gateways.doctype.stancer_settings.api import StancerPaymentsAPI, StancerPayoutsAPI
 
 from erpnext.accounts.page.bank_reconciliation.bank_reconciliation import BankReconciliation
 
 
+if TYPE_CHECKING:
+	from erpnext.accounts.doctype.payment_entry.payment_entry import PaymentEntry
+
+
 def reconcile_stancer_payouts(bank_transactions):
 	stancer_transactions = [
 		transaction
@@ -87,9 +94,10 @@ class StancerReconciliation:
 		found_reference = re.search(
 			r"Ild78-Trans-(?:.*?)Stancer (?:.*?)No(.*?)of", self.bank_transaction.get("description")
 		)
+		payments_api = self.stancer_settings.get_payments_api()
 		if found_reference:
 			reference = found_reference.group(1).strip()
-			payouts_api = StancerPayoutsAPI(self.stancer_settings)
+			payouts_api = self.stancer_settings.get_payouts_api()
 			for payment_reference in self.payment_references:
 				payouts = payouts_api.get_list(params={"payment": payment_reference})
 				for payout in payouts.get("payouts", []):
@@ -98,13 +106,22 @@ class StancerReconciliation:
 						break
 
 		if payout_number:
-			payments = StancerPaymentsAPI(self.stancer_settings).get_list(
-				params={"payout": payout_number, "limit": 100}
-			)
+			payments = payments_api.get_list(params={"payout": payout_number, "limit": 100})
 
 			for payment in payments.get("payments"):
-				self.payments.append(payment.get("id"))
+				self.payments.append(
+					{"id": payment.get("id"), "amount": payment.get("amount"), "fees": payment.get("fees")}
+				)
 
 	def get_payment_references(self):
 		for payment in self.payments:
-			self.documents.append(frappe.get_doc("Payment Entry", self.payment_references[payment]).as_dict())
+			if docname := frappe.db.get_value(
+				"Payment Entry", dict(docstatus=1, reference_no=self.payment_references[payment]("id"))
+			):
+				doc: PaymentEntry = frappe.get_doc("Payment Entry", docname)  # type: ignore
+				if doc.paid_amount == self.payment_references[payment]("amount") and self.payment_references[
+					payment
+				]("fees"):
+					doc = self.stancer_settings.amend_payment_with_fees(doc.name)
+
+				self.documents.append(frappe.get_doc("Payment Entry", docname).as_dict())  # type: ignore