diff --git a/erpnext/manufacturing/doctype/job_card/test_job_card.py b/erpnext/manufacturing/doctype/job_card/test_job_card.py
index 0f429bc27cb..2aece0c677c 100644
--- a/erpnext/manufacturing/doctype/job_card/test_job_card.py
+++ b/erpnext/manufacturing/doctype/job_card/test_job_card.py
@@ -1507,15 +1507,14 @@ class TestJobCard(ERPNextTestSuite):
 			return bom
 
 		rm1 = create_item("RM 1")
-		scrap1 = create_item("Scrap 1")
+		shared_scrap = create_item("Shared Scrap")
 		sfg = create_item("SFG 1")
-		sfg_bom = create_bom(rm1.name, sfg.name, scrap1.name)
+		sfg_bom = create_bom(rm1.name, sfg.name, shared_scrap.name)
 
 		rm2 = create_item("RM 2")
 		fg1 = create_item("FG 1")
-		scrap2 = create_item("Scrap 2")
 		scrap_extra = create_item("Scrap Extra")
-		fg_bom = create_bom(rm2.name, fg1.name, scrap2.name, submit=False)
+		fg_bom = create_bom(rm2.name, fg1.name, shared_scrap.name, submit=False)
 		fg_bom.with_operations = 1
 		fg_bom.track_semi_finished_goods = 1
 
@@ -1596,7 +1595,7 @@ class TestJobCard(ERPNextTestSuite):
 		manufacturing_entry = frappe.get_doc(job_card.make_stock_entry_for_semi_fg_item())
 		manufacturing_entry.submit()
 
-		self.assertEqual(manufacturing_entry.items[2].item_code, scrap1.name)
+		self.assertEqual(manufacturing_entry.items[2].item_code, shared_scrap.name)
 		self.assertEqual(manufacturing_entry.items[2].qty, 9)
 		self.assertEqual(flt(manufacturing_entry.items[2].basic_rate, 3), 5.556)
 		self.assertEqual(manufacturing_entry.items[3].item_code, scrap_extra.name)
@@ -1637,7 +1636,7 @@ class TestJobCard(ERPNextTestSuite):
 		sfg_row = next(row for row in manufacturing_entry.items if row.item_code == sfg.name)
 		self.assertEqual(flt(sfg_row.basic_rate, 3), 95.0)
 
-		self.assertEqual(manufacturing_entry.items[2].item_code, scrap2.name)
+		self.assertEqual(manufacturing_entry.items[2].item_code, shared_scrap.name)
 		self.assertEqual(manufacturing_entry.items[2].qty, 9)
 		self.assertEqual(flt(manufacturing_entry.items[2].basic_rate, 3), 5.278)
 
@@ -2777,6 +2776,18 @@ class TestJobCard(ERPNextTestSuite):
 		self.assertEqual(s.items[3].item_code, "_Test Item")
 		self.assertEqual(s.items[3].transfer_qty, 2)
 
+		frappe.db.set_value(
+			"Stock Entry Detail",
+			s.items[3].name,
+			{"secondary_item_type": None, "is_legacy_scrap_item": 1},
+		)
+
+		from erpnext.stock.doctype.stock_entry.services.manufacturing import ManufactureStockEntry
+
+		stock_entry = frappe.get_doc({"doctype": "Stock Entry", "work_order": self.work_order.name})
+		used_secondary_items = ManufactureStockEntry(stock_entry).get_used_secondary_items()
+		self.assertEqual(used_secondary_items[("_Test Item", "Scrap")], 2)
+
 	@ERPNextTestSuite.change_settings(
 		"Manufacturing Settings", {"overproduction_percentage_for_work_order": 100}
 	)
diff --git a/erpnext/stock/doctype/stock_entry/services/manufacturing.py b/erpnext/stock/doctype/stock_entry/services/manufacturing.py
index 0971ac3b54a..d1b5178c95b 100644
--- a/erpnext/stock/doctype/stock_entry/services/manufacturing.py
+++ b/erpnext/stock/doctype/stock_entry/services/manufacturing.py
@@ -862,6 +862,9 @@ class ManufactureStockEntry(BaseManufactureStockEntry):
 
 		secondary_items = self.get_secondary_items_from_job_card()
 		for row in secondary_items:
+			if row.stock_qty <= 0:
+				continue
+
 			row.uom = row.uom or row.stock_uom
 			row.qty = ceil_qty_if_uom_has_whole_number(row.stock_qty, row.stock_uom)
 			row.transfer_qty = row.qty
@@ -888,33 +891,38 @@ class ManufactureStockEntry(BaseManufactureStockEntry):
 
 	def _adjust_secondary_item_qtys(self, secondary_items, used_secondary_items, pending_qty):
 		for row in secondary_items:
-			row.stock_qty -= flt(used_secondary_items.get(row.item_code))
+			key = (row.item_code, row.secondary_item_type or "")
+			row.stock_qty -= flt(used_secondary_items.get(key))
 			row.stock_qty = row.stock_qty * flt(self.doc.fg_completed_qty) / flt(pending_qty)
-			if used_secondary_items.get(row.item_code):
-				used_secondary_items[row.item_code] -= row.stock_qty
 
 	def get_used_secondary_items(self):
 		data = self._query_used_secondary_items()
 		used_secondary_items = defaultdict(float)
 		for row in data:
-			used_secondary_items[row.item_code] += row.qty
+			secondary_item_type = row.secondary_item_type or ("Scrap" if row.is_legacy_scrap_item else "")
+			key = (row.item_code, secondary_item_type)
+			used_secondary_items[key] += row.qty
 		return used_secondary_items
 
 	def _query_used_secondary_items(self):
 		se = frappe.qb.DocType("Stock Entry")
 		sed = frappe.qb.DocType("Stock Entry Detail")
-		return (
+		query = (
 			frappe.qb.from_(se)
 			.inner_join(sed)
 			.on(sed.parent == se.name)
-			.select(sed.item_code, sed.qty)
+			.select(sed.item_code, sed.secondary_item_type, sed.is_legacy_scrap_item, sed.qty)
 			.where(
 				(se.work_order == self.doc.work_order)
 				& ((sed.secondary_item_type.isnotnull()) | (sed.is_legacy_scrap_item == 1))
 				& (se.docstatus == 1)
 				& (se.purpose.isin(["Repack", "Manufacture"]))
 			)
-		).run(as_dict=1)
+		)
+		if self.doc.job_card:
+			query = query.where(se.job_card == self.doc.job_card)
+
+		return query.run(as_dict=1)
 
 	def get_completed_job_card_qty(self):
 		return flt(min([d.completed_qty for d in self.wo_doc.operations]))