diff --git a/erpnext/stock/doctype/stock_entry/stock_entry.py b/erpnext/stock/doctype/stock_entry/stock_entry.py
index 80552b7c25f..048fa211b6f 100644
--- a/erpnext/stock/doctype/stock_entry/stock_entry.py
+++ b/erpnext/stock/doctype/stock_entry/stock_entry.py
@@ -554,6 +554,13 @@ class StockEntry(StockController, SubcontractingInwardController):
 		for d in self.get("items"):
 			if d.s_warehouse or d.set_basic_rate_manually:
 				continue
+
+			# 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)
 
 		if zero_valuation_items:
@@ -575,7 +582,10 @@ class StockEntry(StockController, SubcontractingInwardController):
 			cost_allocation_per = frappe.get_value(
 				"BOM Secondary Item", d.bom_secondary_item, "cost_allocation_per"
 			)
-			d.basic_rate = (outgoing_items_cost * (cost_allocation_per / 100)) / d.transfer_qty
+			# 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
 
 		if not d.basic_rate and not d.allow_zero_valuation_rate:
 			d.basic_rate = get_valuation_rate(