By default, MyWorks syncs each Shopify order to QuickBooks Online as a single invoice containing all of the order's line items. With the Invoices split by fulfillment option, MyWorks instead creates a separate QuickBooks invoice for each fulfillment in a Shopify order - so you can invoice customers only for the items that have actually shipped.
This is helpful for teams that:
Recognize revenue only when items ship, rather than when the order is placed.
Bill or charge customers per shipment.
Fulfill larger orders in multiple stages over time.
Note: This option is available on the Scale and Soar plans, for Shopify → QuickBooks Online.
How it works
In MyWorks Sync > Settings > Order, set Sync Orders As to Invoices split by fulfillment. When enabled, each new fulfillment in a Shopify order creates its own QuickBooks invoice containing only the items — and quantities — included in that fulfillment.
As additional fulfillments are created in Shopify, MyWorks syncs a new invoice for each one.
Each invoice uses your normal invoice number with the fulfillment number appended — F1, F2, and so on — so it's clear which shipment each invoice represents. Your invoice prefix is still controlled by your existing invoice number settings.
Items that are not yet fulfilled are not yet invoiced.
Example: A Shopify order has 9 products.
2 products ship today (fulfillment #1) → MyWorks creates an invoice ending in F1 with those 2 items.
3 products ship tomorrow (fulfillment #2) → MyWorks creates an invoice ending in F2 with those 3 items - with an invoice date of tomorrow.
4 products remain unfulfilled → no invoice is created for them until they ship.
If every item is fulfilled at once, you'll simply get a single invoice (ending in F1) containing the whole order.
When to use this vs. other order modes
Mode | What it does | Best for |
Standard (single invoice) | One invoice per order, containing all items, synced when the order syncs. | Most stores — invoicing the full order up front. |
Only fulfilled line items | One invoice per order; items are added to that same invoice as we update it when they're fulfilled in Shopify. | Keeping a single invoice per order, but only reflecting shipped items. |
Invoices by fulfillment | A separate invoice for each fulfillment, containing only that shipment's items. | Recognizing revenue and billing per shipment, where each fulfillment should stand on its own. |
If your goal is to defer revenue until items ship but still keep a single order document, you may also want to review our article on recognizing/deferring revenue based on shipment status.
Partial fulfillments, discounts, and shipping
Each fulfillment becomes its own invoice containing only the items and quantities in that specific shipment. Partial quantities are fully supported — if 3 of 10 units of a product ship in a fulfillment, that invoice shows a quantity of 3.
Discounts, taxes, shipping, and other charges are split onto the right invoice whenever they can be tied to specific line items in a fulfillment. Anything that can't be attributed to a specific fulfillment — such as order-level discounts, shipping, tips, and transaction fees — is placed on the first fulfillment invoice synced for the order.
Payments
Shopify lets customers pay only for the items being shipped, so an order may have a separate payment for each fulfillment. MyWorks records each payment in QuickBooks and applies it to the correct fulfillment invoice, so each invoice reflects the payment that corresponds to its shipment.
Refunds
Refunds continue to sync to QuickBooks exactly as they do for any other order — as separate refund receipts. Refunds are not linked to a specific fulfillment invoice.
Important notes
Applies going forward only. Selecting this option doesn't retroactively split orders that already synced as a single invoice - it only affects orders synced from that point on.
Automatic sync statuses. Make sure the relevant order statuses (such as Pending / Fulfilled / Partially Fulfilled) are included under Settings > Order so MyWorks picks the order update up as each fulfillment occurs.