If your store charges import duties or tariffs at checkout, Shopify collects that amount separately from sales tax. MyWorks can sync it into QuickBooks Online as its own line item, so the QuickBooks order total matches what the customer actually paid.
This is off by default. Until you turn it on, duties collected in Shopify aren't included in the QuickBooks order — so the QuickBooks total will be short by the duty amount on any order that charged one.
Turning on duties syncing
Go to MyWorks Sync > Settings > Order in our app in Shopify, and enable Sync Shopify Order Duties as a line item.
You'll find it just below the shipping line item settings.
Choosing the QuickBooks product
Once the setting is enabled, a second option appears: QuickBooks Product for Duties line item. This is the QuickBooks product that will represent duties on the order.
We recommend creating a dedicated non-inventory or service item in QuickBooks — for example "Import Duties" — pointed at whichever account your accountant wants duties tracked in. That keeps duties reportable separately from your product sales.
If you leave this blank, MyWorks will use your default order product instead, so the order still syncs with the correct total.
What it looks like in QuickBooks
The duty amount is added as a single line on the QuickBooks order, described as Shopify Order Duties, with a quantity of 1 and a rate equal to the total duties collected on the Shopify order.
If your QuickBooks company requires a tax code on each line, the duties line is set to your non-taxable / zero-rated code. Duties have already been collected by Shopify, so this makes sure QuickBooks doesn't calculate tax on top of them a second time.
Which orders this applies to
The duties line is added to Invoices, Sales Receipts and Estimates created from your Shopify orders.
If you sync orders as an invoice per fulfillment, duties are added to the first fulfillment's invoice only. Duties are charged once on the order as a whole, not per shipment, so an order that ships in three parts will still show the duty amount once across the three invoices.
Multi-currency orders
If you sell in multiple currencies, the duties line is synced in the same currency the rest of the order syncs in — so a duties line on a CAD invoice is the CAD amount your customer was charged, not a converted home-currency figure.
Refunds
The duties line on the Invoice or Sales Receipt is the duty your customer originally paid, and it stays at that amount. Refunding duties later never rewrites the document QuickBooks already has, so re-syncing an order you have since refunded will not move a total you have already reconciled. The same is true of an order refunded before it ever synced - the sale still carries the duty, and the refund carries the offset.
When you refund duties in Shopify, the Refund Receipt we create in QuickBooks carries its own Shopify Order Duties line for the amount that came back, using the same QuickBooks product as the order. Partial refunds work the same way - each one shows only the duty refunded with it.
This arrived in September 2026. Refunds that synced before then do not have a duties line on them - you can add that adjustment in QuickBooks yourself, or contact us and we can look at re-syncing the refund for you.
Using QuickBooks Desktop?
The same option is available in MyWorks Sync for Shopify and QuickBooks Desktop, under Settings > Order, with the same name and behavior.