diff --git a/erpnext/controllers/stock_controller.py b/erpnext/controllers/stock_controller.py
index 74c835c..61eb0f6 100644
--- a/erpnext/controllers/stock_controller.py
+++ b/erpnext/controllers/stock_controller.py
@@ -156,14 +156,18 @@
 				if self.doctype == "Stock Reconciliation":
 					qty = row.qty
 					type_of_transaction = "Inward"
+					warehouse = row.warehouse
 				else:
-					qty = row.stock_qty
+					qty = row.stock_qty if self.doctype != "Stock Entry" else row.transfer_qty
 					type_of_transaction = get_type_of_transaction(self, row)
+					warehouse = (
+						row.warehouse if self.doctype != "Stock Entry" else row.s_warehouse or row.t_warehouse
+					)
 
 				sn_doc = SerialBatchCreation(
 					{
 						"item_code": row.item_code,
-						"warehouse": row.warehouse,
+						"warehouse": warehouse,
 						"posting_date": self.posting_date,
 						"posting_time": self.posting_time,
 						"voucher_type": self.doctype,
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index 10e3522..3419155 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -982,6 +982,9 @@
 		already_picked_serial_nos = []
 
 		for row in self.items:
+			if row.use_serial_batch_fields and (row.serial_no or row.batch_no):
+				continue
+
 			if not row.s_warehouse:
 				continue
 
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry_utils.py b/erpnext/stock/doctype/stock_entry/stock_entry_utils.py
index 0f67e47..271cbbc 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry_utils.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry_utils.py
@@ -92,9 +92,6 @@
 		else:
 			args.qty = cint(args.qty)
 
-	if args.serial_no or args.batch_no:
-		args.use_serial_batch_fields = True
-
 	# purpose
 	if not args.purpose:
 		if args.source and args.target:
@@ -136,7 +133,7 @@
 	serial_number = args.serial_no
 
 	bundle_id = None
-	if args.serial_no or args.batch_no or args.batches:
+	if not args.use_serial_batch_fields and (args.serial_no or args.batch_no or args.batches):
 		batches = frappe._dict({})
 		if args.batch_no:
 			batches = frappe._dict({args.batch_no: args.qty})
@@ -164,7 +161,11 @@
 			.name
 		)
 
-	args.serial_no = serial_number
+		args["serial_no"] = ""
+		args["batch_no"] = ""
+
+	else:
+		args.serial_no = serial_number
 
 	s.append(
 		"items",
diff --git a/erpnext/stock/doctype/stock_entry/test_stock_entry.py b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
index af91536..6c3faa6 100644
--- a/erpnext/stock/doctype/stock_entry/test_stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
@@ -1596,6 +1596,7 @@
 			qty=4,
 			to_warehouse="_Test Warehouse - _TC",
 			batch_no=batch.name,
+			use_serial_batch_fields=1,
 			do_not_save=True,
 		)
 
@@ -1754,6 +1755,51 @@
 			mr.cancel()
 			mr.delete()
 
+	def test_use_serial_and_batch_fields(self):
+		item = make_item(
+			"Test Use Serial and Batch Item SN Item",
+			{"has_serial_no": 1, "is_stock_item": 1},
+		)
+
+		serial_nos = [
+			"Test Use Serial and Batch Item SN Item - SN 001",
+			"Test Use Serial and Batch Item SN Item - SN 002",
+		]
+
+		se = make_stock_entry(
+			item_code=item.name,
+			qty=2,
+			to_warehouse="_Test Warehouse - _TC",
+			use_serial_batch_fields=1,
+			serial_no="\n".join(serial_nos),
+		)
+
+		self.assertTrue(se.items[0].use_serial_batch_fields)
+		self.assertFalse(se.items[0].serial_no)
+		self.assertTrue(se.items[0].serial_and_batch_bundle)
+
+		for serial_no in serial_nos:
+			self.assertTrue(frappe.db.exists("Serial No", serial_no))
+			self.assertEqual(frappe.db.get_value("Serial No", serial_no, "status"), "Active")
+
+		se1 = make_stock_entry(
+			item_code=item.name,
+			qty=2,
+			from_warehouse="_Test Warehouse - _TC",
+			use_serial_batch_fields=1,
+			serial_no="\n".join(serial_nos),
+		)
+
+		se1.reload()
+
+		self.assertTrue(se1.items[0].use_serial_batch_fields)
+		self.assertFalse(se1.items[0].serial_no)
+		self.assertTrue(se1.items[0].serial_and_batch_bundle)
+
+		for serial_no in serial_nos:
+			self.assertTrue(frappe.db.exists("Serial No", serial_no))
+			self.assertEqual(frappe.db.get_value("Serial No", serial_no, "status"), "Delivered")
+
 
 def make_serialized_item(**args):
 	args = frappe._dict(args)