diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.js b/erpnext/stock/doctype/stock_entry/stock_entry.js
index 47704712594..79ce2312f64 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.js
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.js
@@ -622,7 +622,7 @@ frappe.ui.form.on('Stock Entry Detail', {
 					if(r.message) {
 						var d = locals[cdt][cdn];
 						$.each(r.message, function(k, v) {
-							d[k] = v;
+							frappe.model.set_value(cdt, cdn, k, v); // qty and it's subsequent fields weren't triggered
 						});
 						refresh_field("items");
 						erpnext.stock.select_batch_and_serial_no(frm, d);
diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index f81fa683ba5..00d27ef232b 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -649,6 +649,12 @@ class StockEntry(StockController):
 		gl_entries = super(StockEntry, self).get_gl_entries(warehouse_account)
 
 		total_basic_amount = sum([flt(t.basic_amount) for t in self.get("items") if t.t_warehouse])
+		divide_based_on = total_basic_amount
+
+		if self.get("additional_costs") and not total_basic_amount:
+			# if total_basic_amount is 0, distribute additional charges based on qty
+			divide_based_on = sum(item.qty for item in list(self.get("items")))
+
 		item_account_wise_additional_cost = {}
 
 		for t in self.get("additional_costs"):
@@ -656,8 +662,11 @@ class StockEntry(StockController):
 				if d.t_warehouse:
 					item_account_wise_additional_cost.setdefault((d.item_code, d.name), {})
 					item_account_wise_additional_cost[(d.item_code, d.name)].setdefault(t.expense_account, 0.0)
+
+					multiply_based_on = d.basic_amount if total_basic_amount else d.qty
+
 					item_account_wise_additional_cost[(d.item_code, d.name)][t.expense_account] += \
-						(t.amount * d.basic_amount) / total_basic_amount
+						(t.amount * multiply_based_on) / divide_based_on
 
 		if item_account_wise_additional_cost:
 			for d in self.get("items"):
diff --git a/erpnext/stock/doctype/stock_entry/test_stock_entry.py b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
index eddab5d79dc..ee5f2370987 100644
--- a/erpnext/stock/doctype/stock_entry/test_stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/test_stock_entry.py
@@ -790,6 +790,50 @@ class TestStockEntry(unittest.TestCase):
 			filters={"voucher_type": "Stock Entry", "voucher_no": mr.name}, fieldname="is_opening")
 		self.assertEqual(is_opening, "Yes")
 
+	def test_total_basic_amount_zero(self):
+		se = frappe.get_doc({"doctype":"Stock Entry",
+		"purpose":"Material Receipt",
+		"stock_entry_type":"Material Receipt",
+		"posting_date": nowdate(),
+		"company":"_Test Company with perpetual inventory",
+		"items":[
+			{
+				"item_code":"Basil Leaves",
+				"description":"Basil Leaves",
+				"qty": 1,
+				"basic_rate": 0,
+				"uom":"Nos",
+				"t_warehouse": "Stores - TCP1",
+				"allow_zero_valuation_rate": 1,
+				"cost_center": "Main - TCP1"
+			 },
+			 {
+				"item_code":"Basil Leaves",
+				"description":"Basil Leaves",
+				"qty": 2,
+				"basic_rate": 0,
+				"uom":"Nos",
+				"t_warehouse": "Stores - TCP1",
+				"allow_zero_valuation_rate": 1,
+				"cost_center": "Main - TCP1"
+			 },
+			 ],
+		"additional_costs":[
+			{"expense_account":"Miscellaneous Expenses - TCP1",
+			"amount":100,
+			"description": "miscellanous"}
+			]
+		})
+		se.insert()
+		se.submit()
+
+		self.check_gl_entries("Stock Entry", se.name,
+			sorted([
+				["Stock Adjustment - TCP1", 100.0, 0.0],
+				["Miscellaneous Expenses - TCP1", 0.0, 100.0]
+			])
+		)
+
 def make_serialized_item(item_code=None, serial_no=None, target_warehouse=None):
 	se = frappe.copy_doc(test_records[0])
 	se.get("items")[0].item_code = item_code or "_Test Serialized Item With Series"