diff --git a/erpnext/accounts/doctype/payment_entry/payment_entry.py b/erpnext/accounts/doctype/payment_entry/payment_entry.py
index eb1673a8798..350e8b700a9 100644
--- a/erpnext/accounts/doctype/payment_entry/payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/payment_entry.py
@@ -1285,8 +1285,11 @@ class PaymentEntry(AccountsController):
 
 	def make_gl_entries(self, cancel=0, adv_adj=0):
 		gl_entries = self.build_gl_map()
-		gl_entries = process_gl_map(gl_entries)
-		make_gl_entries(gl_entries, cancel=cancel, adv_adj=adv_adj)
+
+		merge_entries = frappe.get_single_value("Accounts Settings", "merge_similar_account_heads")
+
+		gl_entries = process_gl_map(gl_entries, merge_entries=merge_entries)
+		make_gl_entries(gl_entries, cancel=cancel, adv_adj=adv_adj, merge_entries=merge_entries)
 		if cancel:
 			cancel_exchange_gain_loss_journal(frappe._dict(doctype=self.doctype, name=self.name))
 		else:
diff --git a/erpnext/accounts/doctype/payment_entry/test_payment_entry.py b/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
index 355aa46ea05..f6c240c0714 100644
--- a/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
+++ b/erpnext/accounts/doctype/payment_entry/test_payment_entry.py
@@ -1045,6 +1045,7 @@ class TestPaymentEntry(IntegrationTestCase):
 		)
 
 	def test_gl_of_multi_currency_payment_with_taxes(self):
+		frappe.db.set_single_value("Accounts Settings", "merge_similar_account_heads", 1)
 		payment_entry = create_payment_entry(
 			party="_Test Supplier USD", paid_to="_Test Payable USD - _TC", save=True
 		)
@@ -1606,6 +1607,96 @@ class TestPaymentEntry(IntegrationTestCase):
 		self.voucher_no = pe.name
 		self.check_gl_entries()
 
+	def test_payment_entry_merges_gl_entries_with_same_account_head(self):
+		"""
+		Test that Payment Entry merges GL entries with same account head
+		when 'Merge Similar Account Heads' setting is enabled.
+		"""
+		frappe.db.set_single_value("Accounts Settings", "merge_similar_account_heads", 1)
+
+		pe = create_payment_entry(
+			party_type="Supplier",
+			party="_Test Supplier",
+			paid_from="_Test Bank - _TC",
+			paid_to="Creditors - _TC",
+		)
+
+		pe.append(
+			"deductions",
+			{
+				"account": "Write Off - _TC",
+				"cost_center": "_Test Cost Center - _TC",
+				"amount": 50,
+			},
+		)
+
+		pe.append(
+			"deductions",
+			{
+				"account": "Write Off - _TC",
+				"cost_center": "_Test Cost Center - _TC",
+				"amount": 30,
+			},
+		)
+
+		pe.save()
+		pe.submit()
+
+		gl_entries = frappe.db.get_all(
+			"GL Entry",
+			filters={"voucher_no": pe.name, "account": "Write Off - _TC", "is_cancelled": 0},
+			fields=["debit", "credit"],
+		)
+
+		self.assertEqual(len(gl_entries), 1)
+		self.assertEqual(gl_entries[0].debit, 80)
+
+	def test_payment_entry_does_not_merge_gl_entries_when_setting_disabled(self):
+		"""
+		Test that Payment Entry does NOT merge GL entries
+		when 'Merge Similar Account Heads' is disabled.
+		"""
+
+		frappe.db.set_single_value("Accounts Settings", "merge_similar_account_heads", 0)
+
+		pe = create_payment_entry(
+			party_type="Supplier",
+			party="_Test Supplier",
+			paid_from="_Test Bank - _TC",
+			paid_to="Creditors - _TC",
+		)
+
+		pe.append(
+			"deductions",
+			{
+				"account": "Write Off - _TC",
+				"cost_center": "_Test Cost Center - _TC",
+				"amount": 50,
+			},
+		)
+
+		pe.append(
+			"deductions",
+			{
+				"account": "Write Off - _TC",
+				"cost_center": "_Test Cost Center - _TC",
+				"amount": 30,
+			},
+		)
+
+		pe.save()
+		pe.submit()
+
+		gl_entries = frappe.db.get_all(
+			"GL Entry",
+			filters={"voucher_no": pe.name, "account": "Write Off - _TC", "is_cancelled": 0},
+			fields=["debit", "credit"],
+		)
+
+		self.assertEqual(len(gl_entries), 2)
+
+		frappe.db.set_single_value("Accounts Settings", "merge_similar_account_heads", 1)
+
 	def check_pl_entries(self):
 		ple = frappe.qb.DocType("Payment Ledger Entry")
 		pl_entries = (
diff --git a/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py b/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
index adb11f8d615..cb771bdc35a 100644
--- a/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
+++ b/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
@@ -1498,6 +1498,8 @@ class TestPurchaseInvoice(IntegrationTestCase, StockTestMixin):
 	def test_purchase_invoice_advance_taxes(self):
 		from erpnext.accounts.doctype.payment_entry.payment_entry import get_payment_entry
 
+		frappe.db.set_single_value("Accounts Settings", "merge_similar_account_heads", 1)
+
 		company = "_Test Company"
 
 		tds_account_args = {