diff --git a/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py b/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
index 76fbfd2f4e2..4d62c0d354d 100644
--- a/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
+++ b/erpnext/accounts/doctype/purchase_invoice/test_purchase_invoice.py
@@ -2494,6 +2494,34 @@ class TestPurchaseInvoice(FrappeTestCase, StockTestMixin):
 		self.assertEqual(len(actual), 3)
 		self.assertEqual(expected, actual)
 
+	def test_invoice_against_returned_pr(self):
+		from erpnext.stock.doctype.item.test_item import make_item
+		from erpnext.stock.doctype.purchase_receipt.purchase_receipt import (
+			make_purchase_invoice as make_purchase_invoice_from_pr,
+		)
+		from erpnext.stock.doctype.purchase_receipt.purchase_receipt import (
+			make_purchase_return_against_rejected_warehouse,
+		)
+
+		item = make_item("_Test Item For Invoice Against Returned PR", properties={"is_stock_item": 1}).name
+
+		original_value = frappe.db.get_single_value(
+			"Buying Settings", "bill_for_rejected_quantity_in_purchase_invoice"
+		)
+		frappe.db.set_single_value("Buying Settings", "bill_for_rejected_quantity_in_purchase_invoice", 0)
+
+		pr = make_purchase_receipt(item_code=item, qty=5, rejected_qty=5, rate=100)
+		pr_return = make_purchase_return_against_rejected_warehouse(pr.name)
+		pr_return.submit()
+
+		pi = make_purchase_invoice_from_pr(pr.name)
+		pi.save()
+		self.assertEqual(pi.items[0].qty, 5.0)
+
+		frappe.db.set_single_value(
+			"Buying Settings", "bill_for_rejected_quantity_in_purchase_invoice", original_value
+		)
+
 
 def set_advance_flag(company, flag, default_account):
 	frappe.db.set_value(
diff --git a/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py b/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
index 22d7012cc8b..44e0145ea6c 100644
--- a/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
+++ b/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
@@ -1183,6 +1183,9 @@ def make_purchase_invoice(source_name, target_doc=None, args=None):
 			return pending_qty, 0
 
 		returned_qty = flt(returned_qty_map.get(item_row.name, 0))
+		if item_row.rejected_qty and returned_qty:
+			returned_qty -= item_row.rejected_qty
+
 		if returned_qty:
 			if returned_qty >= pending_qty:
 				pending_qty = 0