diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index 48821c2bb77402b72c8969b2cf73b4426736e147..df9aef69bd05b5ca2ca9a5337a70e3e802d6d861 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -2704,13 +2704,14 @@ def add_income_discount_loss(pe, doc, total_discount_percent) -> float:
 	"""Add loss on income discount in base currency."""
 	precision = doc.precision("total")
 	base_loss_on_income = doc.get("base_total") * (total_discount_percent / 100)
+	positive_negative = -1 if pe.payment_type == "Pay" else 1
 
 	pe.append(
 		"deductions",
 		{
 			"account": frappe.get_cached_value("Company", pe.company, "default_discount_account"),
 			"cost_center": pe.cost_center or frappe.get_cached_value("Company", pe.company, "cost_center"),
-			"amount": flt(base_loss_on_income, precision),
+			"amount": flt(base_loss_on_income, precision) * positive_negative,
 		},
 	)
 
@@ -2722,6 +2723,7 @@ def add_tax_discount_loss(pe, doc, total_discount_percentage) -> float:
 	tax_discount_loss = {}
 	base_total_tax_loss = 0
 	precision = doc.precision("tax_amount_after_discount_amount", "taxes")
+	positive_negative = -1 if pe.payment_type == "Pay" else 1
 
 	# The same account head could be used more than once
 	for tax in doc.get("taxes", []):
@@ -2744,8 +2746,9 @@ def add_tax_discount_loss(pe, doc, total_discount_percentage) -> float:
 			"deductions",
 			{
 				"account": account,
-				"cost_center": pe.cost_center or frappe.get_cached_value("Company", pe.company, "cost_center"),
-				"amount": flt(loss, precision),
+				"cost_center": pe.cost_center
+				or frappe.get_cached_value("Company", pe.company, "cost_center"),
+				"amount": flt(loss, precision) * positive_negative,
 			},
 		)
 
diff --git a/erpnext/accounts/doctype/payment_entry/test_payment_entry.py b/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
index 15dbaf9e9c451be3721c117795c9fd1c60de3fd1..26a1235b2edbf10482b9f829352ac98d42b59f4c 100644
--- a/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
@@ -282,6 +282,48 @@ class TestPaymentEntry(FrappeTestCase):
 		self.assertEqual(si.payment_schedule[0].paid_amount, 200.0)
 		self.assertEqual(si.payment_schedule[1].paid_amount, 36.0)
 
+	def test_payment_entry_against_payment_terms_with_discount_on_pi(self):
+		pi = make_purchase_invoice(do_not_save=1)
+		create_payment_terms_template_with_discount()
+		pi.payment_terms_template = "Test Discount Template"
+
+		frappe.db.set_value("Company", pi.company, "default_discount_account", "Write Off - _TC")
+
+		pi.append(
+			"taxes",
+			{
+				"charge_type": "On Net Total",
+				"account_head": "_Test Account Service Tax - _TC",
+				"cost_center": "_Test Cost Center - _TC",
+				"description": "Service Tax",
+				"rate": 18,
+			},
+		)
+		pi.save()
+		pi.submit()
+
+		frappe.db.set_single_value("Accounts Settings", "book_tax_discount_loss", 1)
+		pe_with_tax_loss = get_payment_entry("Purchase Invoice", pi.name, bank_account="_Test Cash - _TC")
+
+		self.assertEqual(pe_with_tax_loss.references[0].payment_term, "30 Credit Days with 10% Discount")
+		self.assertEqual(pe_with_tax_loss.payment_type, "Pay")
+		self.assertEqual(pe_with_tax_loss.references[0].allocated_amount, 295.0)
+		self.assertEqual(pe_with_tax_loss.paid_amount, 265.5)
+		self.assertEqual(pe_with_tax_loss.difference_amount, 0)
+		self.assertEqual(pe_with_tax_loss.deductions[0].amount, -25.0)  # Loss on Income
+		self.assertEqual(pe_with_tax_loss.deductions[1].amount, -4.5)  # Loss on Tax
+		self.assertEqual(pe_with_tax_loss.deductions[1].account, "_Test Account Service Tax - _TC")
+
+		frappe.db.set_single_value("Accounts Settings", "book_tax_discount_loss", 0)
+		pe = get_payment_entry("Purchase Invoice", pi.name, bank_account="_Test Cash - _TC")
+
+		self.assertEqual(pe.references[0].payment_term, "30 Credit Days with 10% Discount")
+		self.assertEqual(pe.payment_type, "Pay")
+		self.assertEqual(pe.references[0].allocated_amount, 295.0)
+		self.assertEqual(pe.paid_amount, 265.5)
+		self.assertEqual(pe.deductions[0].amount, -29.5)
+		self.assertEqual(pe.difference_amount, 0)
+
 	def test_payment_entry_against_payment_terms_with_discount(self):
 		si = create_sales_invoice(do_not_save=1, qty=1, rate=200)
 		create_payment_terms_template_with_discount()