diff --git a/erpnext/accounts/doctype/purchase_invoice/purchase_invoice.py b/erpnext/accounts/doctype/purchase_invoice/purchase_invoice.py
index 71a0da59520..65d753776d1 100644
--- a/erpnext/accounts/doctype/purchase_invoice/purchase_invoice.py
+++ b/erpnext/accounts/doctype/purchase_invoice/purchase_invoice.py
@@ -1709,6 +1709,9 @@ class PurchaseInvoice(BuyingController):
 		self.db_set("release_date", None)
 
 	def set_tax_withholding(self):
+		self.set("advance_tax", [])
+		self.set("tax_withheld_vouchers", [])
+
 		if not self.apply_tds:
 			return
 
@@ -1750,8 +1753,6 @@ class PurchaseInvoice(BuyingController):
 			self.remove(d)
 
 		## Add pending vouchers on which tax was withheld
-		self.set("tax_withheld_vouchers", [])
-
 		for voucher_no, voucher_details in voucher_wise_amount.items():
 			self.append(
 				"tax_withheld_vouchers",
@@ -1766,7 +1767,6 @@ class PurchaseInvoice(BuyingController):
 		self.calculate_taxes_and_totals()
 
 	def allocate_advance_tds(self, tax_withholding_details, advance_taxes):
-		self.set("advance_tax", [])
 		for tax in advance_taxes:
 			allocated_amount = 0
 			pending_amount = flt(tax.tax_amount - tax.allocated_amount)
diff --git a/erpnext/accounts/doctype/tax_withholding_category/tax_withholding_category.py b/erpnext/accounts/doctype/tax_withholding_category/tax_withholding_category.py
index 1549b45d004..95381eaa1f7 100644
--- a/erpnext/accounts/doctype/tax_withholding_category/tax_withholding_category.py
+++ b/erpnext/accounts/doctype/tax_withholding_category/tax_withholding_category.py
@@ -268,6 +268,11 @@ def get_tax_amount(party_type, parties, inv, tax_details, posting_date, pan_no=N
 	vouchers, voucher_wise_amount = get_invoice_vouchers(
 		parties, tax_details, inv.company, party_type=party_type
 	)
+
+	payment_entry_vouchers = get_payment_entry_vouchers(
+		parties, tax_details, inv.company, party_type=party_type
+	)
+
 	advance_vouchers = get_advance_vouchers(
 		parties,
 		company=inv.company,
@@ -275,7 +280,8 @@ def get_tax_amount(party_type, parties, inv, tax_details, posting_date, pan_no=N
 		to_date=tax_details.to_date,
 		party_type=party_type,
 	)
-	taxable_vouchers = vouchers + advance_vouchers
+
+	taxable_vouchers = vouchers + advance_vouchers + payment_entry_vouchers
 	tax_deducted_on_advances = 0
 
 	if inv.doctype == "Purchase Invoice":
@@ -387,6 +393,20 @@ def get_invoice_vouchers(parties, tax_details, company, party_type="Supplier"):
 	return vouchers, voucher_wise_amount
 
 
+def get_payment_entry_vouchers(parties, tax_details, company, party_type="Supplier"):
+	payment_entry_filters = {
+		"party_type": party_type,
+		"party": ("in", parties),
+		"docstatus": 1,
+		"apply_tax_withholding_amount": 1,
+		"posting_date": ["between", (tax_details.from_date, tax_details.to_date)],
+		"tax_withholding_category": tax_details.get("tax_withholding_category"),
+		"company": company,
+	}
+
+	return frappe.db.get_all("Payment Entry", filters=payment_entry_filters, pluck="name")
+
+
 def get_advance_vouchers(parties, company=None, from_date=None, to_date=None, party_type="Supplier"):
 	"""
 	Use Payment Ledger to fetch unallocated Advance Payments