diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.js b/erpnext/stock/doctype/stock_entry/stock_entry.js
index 6ff0ed93885c49401e9ba0b1a6cb0794aa702948..29c174c09fa34f4a83bae65d4cb21dbbabde0c9d 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.js
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.js
@@ -571,7 +571,7 @@ frappe.ui.form.on("Stock Entry", {
 		const item = locals[cdt][cdn];
 		item.transfer_qty = flt(item.qty) * flt(item.conversion_factor);
 
-		const args = {
+		let args = {
 			item_code: item.item_code,
 			posting_date: frm.doc.posting_date,
 			posting_time: frm.doc.posting_time,
@@ -585,6 +585,10 @@ frappe.ui.form.on("Stock Entry", {
 			allow_zero_valuation: 1,
 		};
 
+		if (item.batch_no && frm.doc.purpose == "Material Receipt") {
+			args.qty = Math.abs(args.qty) * -1;
+		}
+
 		if (item.item_code || item.serial_no) {
 			frappe.call({
 				method: "erpnext.stock.utils.get_incoming_rate",