diff --git a/erpnext/stock/doctype/stock_entry/test_stock_entry.py b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
index 2cd3fde5f84..af4e0f42c9a 100644
--- a/erpnext/stock/doctype/stock_entry/test_stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
@@ -2759,6 +2759,55 @@ class TestStockEntry(ERPNextTestSuite):
 		self.assertRaises(QualityInspectionRequiredError, receipt("").submit)
 		self.assertRaises(QualityInspectionRequiredError, receipt("Scrap").submit)
 
+	def test_manufacture_balances_secondary_item_added_without_a_bom(self):
+		"""A secondary item with no BOM link is costed out of the finished good, as legacy scrap was."""
+		rm_item = make_item(properties={"is_stock_item": 1}).name
+		fg_item = make_item(properties={"is_stock_item": 1}).name
+		scrap_item = make_item(properties={"is_stock_item": 1, "valuation_rate": 20}).name
+		warehouse = "_Test Warehouse - _TC"
+
+		make_stock_entry(item_code=rm_item, target=warehouse, qty=10, basic_rate=100)
+
+		se = frappe.new_doc("Stock Entry")
+		se.purpose = se.stock_entry_type = "Manufacture"
+		se.company = "_Test Company"
+		se.append(
+			"items", {"item_code": rm_item, "s_warehouse": warehouse, "qty": 10, "conversion_factor": 1}
+		)
+		se.append(
+			"items",
+			{
+				"item_code": fg_item,
+				"t_warehouse": warehouse,
+				"qty": 10,
+				"is_finished_item": 1,
+				"conversion_factor": 1,
+			},
+		)
+		se.append(
+			"items",
+			{
+				"item_code": scrap_item,
+				"t_warehouse": warehouse,
+				"qty": 5,
+				"secondary_item_type": "Scrap",
+				"conversion_factor": 1,
+			},
+		)
+		se.save()
+
+		scrap_row = se.items[2]
+		self.assertEqual(flt(scrap_row.basic_rate), 20.0)
+		self.assertEqual(flt(scrap_row.basic_amount), 100.0)
+
+		fg_row = se.items[1]
+		self.assertEqual(flt(fg_row.basic_rate), 90.0)
+		self.assertEqual(flt(fg_row.basic_amount), 900.0)
+
+		self.assertEqual(flt(se.total_incoming_value), 1000.0)
+		self.assertEqual(flt(se.total_outgoing_value), 1000.0)
+		self.assertEqual(flt(se.value_difference), 0.0)
+
 	def _make_wo_for_free_raw_material(self, rm_item, fg_item, bom_no):
 		from erpnext.manufacturing.doctype.work_order.test_work_order import make_wo_order_test_record
 		from erpnext.manufacturing.doctype.work_order.work_order import (