diff --git a/erpnext/controllers/buying_controller.py b/erpnext/controllers/buying_controller.py
index 5627dffea95..0f74ea12348 100644
--- a/erpnext/controllers/buying_controller.py
+++ b/erpnext/controllers/buying_controller.py
@@ -461,7 +461,17 @@ class BuyingController(SubcontractingController):
 						get_conversion_factor(item.item_code, item.uom).get("conversion_factor") or 1.0
 					)
 
-				net_rate = item.qty * item.base_net_rate
+				net_rate = (
+					flt(
+						(item.base_net_amount / item.received_qty) * item.qty,
+						item.precision("base_net_amount"),
+					)
+					if item.received_qty
+					and frappe.get_single_value(
+						"Buying Settings", "bill_for_rejected_quantity_in_purchase_invoice"
+					)
+					else item.base_net_amount
+				)
 				if item.sales_incoming_rate:  # for internal transfer
 					net_rate = item.qty * item.sales_incoming_rate
 
diff --git a/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py b/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
index ae372313380..507b5e17360 100644
--- a/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
+++ b/erpnext/stock/doctype/purchase_receipt/purchase_receipt.py
@@ -562,7 +562,14 @@ class PurchaseReceipt(BuyingController):
 				else flt(item.net_amount, item.precision("net_amount"))
 			)
 
-			outgoing_amount = item.qty * item.base_net_rate
+			outgoing_amount = (
+				flt((item.base_net_amount / item.received_qty) * item.qty, item.precision("base_net_amount"))
+				if item.received_qty
+				and frappe.get_single_value(
+					"Buying Settings", "bill_for_rejected_quantity_in_purchase_invoice"
+				)
+				else item.base_net_amount
+			)
 			if self.is_internal_transfer() and item.valuation_rate:
 				outgoing_amount = abs(get_stock_value_difference(self.name, item.name, item.from_warehouse))
 				credit_amount = outgoing_amount