diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index ae536b8dc42..ea62554e642 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -1379,6 +1379,17 @@ class StockEntry(StockController, SubcontractingInwardController):
 		for d in self.get("items"):
 			if d.s_warehouse or d.set_basic_rate_manually:
 				continue
+<<<<<<< HEAD
+=======
+
+			# Zero-qty secondary items carry no inventory value; skip rate calculation
+			if d.secondary_item_type and flt(d.transfer_qty) == 0:
+				d.basic_rate = 0.0
+				d.basic_amount = 0.0
+				continue
+
+			self._set_incoming_item_rate(d, outgoing_items_cost, raise_error_if_no_rate, zero_valuation_items)
+>>>>>>> de3df6bcef (fix(manufacture): preserve user-entered rate for secondary items with zero cost allocation)
 
 			if d.allow_zero_valuation_rate and d.basic_rate and self.purpose != "Receive from Customer":
 				d.basic_rate = 0.0
@@ -1399,9 +1410,22 @@ class StockEntry(StockController, SubcontractingInwardController):
 				)
 				d.basic_rate = (outgoing_items_cost * (cost_allocation_per / 100)) / d.transfer_qty
 
+<<<<<<< HEAD
 			if not d.basic_rate and not d.allow_zero_valuation_rate:
 				if self.is_new():
 					raise_error_if_no_rate = False
+=======
+			if self.bom_no:
+				d.basic_rate *= frappe.get_value("BOM", self.bom_no, "cost_allocation_per") / 100
+		elif d.secondary_item_type and d.bom_secondary_item:
+			cost_allocation_per = frappe.get_value(
+				"BOM Secondary Item", d.bom_secondary_item, "cost_allocation_per"
+			)
+			# Only recalculate when cost is actually allocated; otherwise preserve the
+			# user-entered rate (or fall through to get_valuation_rate below)
+			if cost_allocation_per and flt(d.transfer_qty):
+				d.basic_rate = (outgoing_items_cost * (cost_allocation_per / 100)) / d.transfer_qty
+>>>>>>> de3df6bcef (fix(manufacture): preserve user-entered rate for secondary items with zero cost allocation)
 
 				d.basic_rate = get_valuation_rate(
 					d.item_code,