diff --git a/erpnext/manufacturing/doctype/manufacturing_settings/manufacturing_settings.json b/erpnext/manufacturing/doctype/manufacturing_settings/manufacturing_settings.json
index 98cb7d8fe88..634eabc9a41 100644
--- a/erpnext/manufacturing/doctype/manufacturing_settings/manufacturing_settings.json
+++ b/erpnext/manufacturing/doctype/manufacturing_settings/manufacturing_settings.json
@@ -242,14 +242,14 @@
    "depends_on": "eval:doc.backflush_raw_materials_based_on == \"BOM\"",
    "fieldname": "validate_components_quantities_per_bom",
    "fieldtype": "Check",
-   "label": "Validate Components Quantities Per BOM"
+   "label": "Validate Components and Quantities Per BOM"
   }
  ],
  "icon": "icon-wrench",
  "index_web_pages_for_search": 1,
  "issingle": 1,
  "links": [],
- "modified": "2024-09-02 12:12:03.132567",
+ "modified": "2025-01-02 12:46:33.520853",
  "modified_by": "Administrator",
  "module": "Manufacturing",
  "name": "Manufacturing Settings",
@@ -267,4 +267,4 @@
  "sort_order": "DESC",
  "states": [],
  "track_changes": 1
-}
+}
\ No newline at end of file
diff --git a/erpnext/manufacturing/doctype/work_order/test_work_order.py b/erpnext/manufacturing/doctype/work_order/test_work_order.py
index 702c38bdf82..e1927747538 100644
--- a/erpnext/manufacturing/doctype/work_order/test_work_order.py
+++ b/erpnext/manufacturing/doctype/work_order/test_work_order.py
@@ -2417,6 +2417,56 @@ class TestWorkOrder(IntegrationTestCase):
 
 		frappe.db.set_single_value("Manufacturing Settings", "validate_components_quantities_per_bom", 0)
 
+	def test_components_as_per_bom_for_manufacture_entry(self):
+		frappe.db.set_single_value("Manufacturing Settings", "backflush_raw_materials_based_on", "BOM")
+		frappe.db.set_single_value("Manufacturing Settings", "validate_components_quantities_per_bom", 1)
+
+		fg_item = "Test FG Item For Component Validation 1"
+		source_warehouse = "Stores - _TC"
+		raw_materials = ["Test Component Validation RM Item 11", "Test Component Validation RM Item 12"]
+
+		make_item(fg_item, {"is_stock_item": 1})
+		for item in raw_materials:
+			make_item(item, {"is_stock_item": 1})
+			test_stock_entry.make_stock_entry(
+				item_code=item,
+				target=source_warehouse,
+				qty=10,
+				basic_rate=100,
+			)
+
+		make_bom(item=fg_item, source_warehouse=source_warehouse, raw_materials=raw_materials)
+
+		wo = make_wo_order_test_record(
+			item=fg_item,
+			qty=10,
+			source_warehouse=source_warehouse,
+		)
+
+		transfer_entry = frappe.get_doc(make_stock_entry(wo.name, "Material Transfer for Manufacture", 10))
+		transfer_entry.save()
+		transfer_entry.remove(transfer_entry.items[0])
+
+		self.assertRaises(frappe.ValidationError, transfer_entry.save)
+
+		transfer_entry = frappe.get_doc(make_stock_entry(wo.name, "Material Transfer for Manufacture", 10))
+		transfer_entry.save()
+		transfer_entry.submit()
+
+		manufacture_entry = frappe.get_doc(make_stock_entry(wo.name, "Manufacture", 10))
+		manufacture_entry.save()
+
+		manufacture_entry.remove(manufacture_entry.items[0])
+
+		self.assertRaises(frappe.ValidationError, manufacture_entry.save)
+		manufacture_entry.delete()
+
+		manufacture_entry = frappe.get_doc(make_stock_entry(wo.name, "Manufacture", 10))
+		manufacture_entry.save()
+		manufacture_entry.submit()
+
+		frappe.db.set_single_value("Manufacturing Settings", "validate_components_quantities_per_bom", 0)
+
 
 def make_operation(**kwargs):
 	kwargs = frappe._dict(kwargs)
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index aa112731c54..1fb36d9c963 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -236,7 +236,7 @@ class StockEntry(StockController):
 		self.validate_serialized_batch()
 		self.calculate_rate_and_amount()
 		self.validate_putaway_capacity()
-		self.validate_component_quantities()
+		self.validate_component_and_quantities()
 
 		if self.get("purpose") != "Manufacture":
 			# ignore scrap item wh difference and empty source/target wh
@@ -766,7 +766,7 @@ class StockEntry(StockController):
 					title=_("Insufficient Stock"),
 				)
 
-	def validate_component_quantities(self):
+	def validate_component_and_quantities(self):
 		if self.purpose not in ["Manufacture", "Material Transfer for Manufacture"]:
 			return
 
@@ -779,20 +779,31 @@ class StockEntry(StockController):
 		raw_materials = self.get_bom_raw_materials(self.fg_completed_qty)
 
 		precision = frappe.get_precision("Stock Entry Detail", "qty")
-		for row in self.items:
-			if not row.s_warehouse:
-				continue
-
-			if details := raw_materials.get(row.item_code):
-				if flt(details.get("qty"), precision) != flt(row.qty, precision):
+		for item_code, details in raw_materials.items():
+			if matched_item := self.get_matched_items(item_code):
+				if flt(details.get("qty"), precision) != flt(matched_item.qty, precision):
 					frappe.throw(
 						_("For the item {0}, the quantity should be {1} according to the BOM {2}.").format(
-							frappe.bold(row.item_code),
-							flt(details.get("qty"), precision),
+							frappe.bold(item_code),
+							flt(details.get("qty")),
 							get_link_to_form("BOM", self.bom_no),
 						),
 						title=_("Incorrect Component Quantity"),
 					)
+			else:
+				frappe.throw(
+					_("According to the BOM {0}, the Item '{1}' is missing in the stock entry.").format(
+						get_link_to_form("BOM", self.bom_no), frappe.bold(item_code)
+					),
+					title=_("Missing Item"),
+				)
+
+	def get_matched_items(self, item_code):
+		for row in self.items:
+			if row.item_code == item_code:
+				return row
+
+		return {}
 
 	@frappe.whitelist()
 	def get_stock_and_rate(self):