diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index b7417eb72e1..707e7ebc461 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -1452,23 +1452,15 @@ class StockEntry(StockController, SubcontractingInwardController):
 			return
 
 		precision = self.precision("process_loss_qty")
-		if self.work_order:
-			data = frappe.get_all(
-				"Work Order Operation",
-				filters={"parent": self.work_order},
-				fields=[{"MAX": "process_loss_qty", "as": "process_loss_qty"}],
+		process_loss_qty = self.get_pending_process_loss_qty()
+		if process_loss_qty and flt(self.process_loss_qty, precision) != flt(process_loss_qty, precision):
+			self.process_loss_qty = flt(process_loss_qty, precision)
+
+			frappe.msgprint(
+				_("The Process Loss Qty has been reset as per the job card's Process Loss Qty"),
+				alert=True,
 			)
 
-			if data and data[0].process_loss_qty:
-				process_loss_qty = data[0].process_loss_qty
-				if flt(self.process_loss_qty, precision) != flt(process_loss_qty, precision):
-					self.process_loss_qty = flt(process_loss_qty, precision)
-
-					frappe.msgprint(
-						_("The Process Loss Qty has been reset as per the job card's Process Loss Qty"),
-						alert=True,
-					)
-
 		if not self.process_loss_percentage and not self.process_loss_qty:
 			self.process_loss_percentage = frappe.get_cached_value(
 				"BOM", self.bom_no, "process_loss_percentage"
@@ -1483,6 +1475,23 @@ class StockEntry(StockController, SubcontractingInwardController):
 				(flt(self.process_loss_qty) / flt(self.fg_completed_qty)) * 100
 			)
 
+	def get_pending_process_loss_qty(self):
+		"""Loss this entry should still book: the job card's unbooked loss when the entry
+		belongs to one, else the largest operation loss on the work order (legacy flow)."""
+		if self.job_card:
+			job_card = frappe.get_doc("Job Card", self.job_card)
+			return max(flt(job_card.process_loss_qty) - flt(job_card.get_consumed_process_loss()), 0)
+
+		if self.work_order:
+			data = frappe.get_all(
+				"Work Order Operation",
+				filters={"parent": self.work_order},
+				fields=[{"MAX": "process_loss_qty", "as": "process_loss_qty"}],
+			)
+			return flt(data[0].process_loss_qty) if data else 0
+
+		return 0
+
 	def set_work_order_details(self):
 		if self.work_order:
 			# common validations