set the target.ignore_pricing_rule to 0
diff --git a/erpnext/selling/doctype/quotation/quotation.py b/erpnext/selling/doctype/quotation/quotation.py
index 3c8add4..c180c41 100644
--- a/erpnext/selling/doctype/quotation/quotation.py
+++ b/erpnext/selling/doctype/quotation/quotation.py
@@ -91,7 +91,9 @@
if customer:
target.customer = customer.name
target.customer_name = customer.customer_name
- target.ignore_pricing_rule = 1
+ # changed from 1 to 0, because margin is applied based on pricing rule.
+ # User will manually disabled pricing rule on sales order.
+ target.ignore_pricing_rule = 0
target.flags.ignore_permissions = ignore_permissions
target.run_method("set_missing_values")
target.run_method("calculate_taxes_and_totals")