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ERP & Accounting
Integrate QuickBooks With Your Shipping and Fulfillment Software
Unlock a cleaner path from order to books. The ShipStation integration with QuickBooks Online helps you ship with more control, send shipped order data into QuickBooks Online, choose invoices or sales receipts, compare rates, and cut manual work across your fulfillment flow.
Key integration features
- Send shipped orders to QuickBooks
- Choose invoices or sales receipts
- Select stores that transmit data
- Match products by SKU
- Export customer and tax data
About
QuickBooks is accounting software from Intuit for small businesses and self-employed professionals. It is known for invoicing, expense tracking, payments, reporting, and day-to-day bookkeeping, with QuickBooks Online serving cloud-based workflows and desktop products serving separate needs.
For businesses using US-based QuickBooks Online, the ShipStation integration keeps fulfillment and accounting moving in the same direction. Orders stay managed in ShipStation, shipped order data moves into QuickBooks Online, and your team spends less time retyping completed shipments or cleaning up records later.
That means stronger control at month-end and fewer handoff mistakes during busy weeks. ShipStation lets you choose whether shipped orders become sales receipts or invoices, decide which stores transmit data, map products by SKU, create or update customer records, and record sales tax with your selected Tax Agencies. If your store, accounting records, and shipping workflow all need to stay aligned, ShipStation gives you one place to ship while keeping QuickBooks Online current on what already went out the door.
Why QuickBooks users choose ShipStation
Move beyond basic shipping and fulfillment tools with ShipStation
STEP 1
Go to Account Settings, select Integration Partners from the sidebar, and choose the Connect button for QuickBooks Online to start the connection.
STEP 2
Click Connect to QuickBooks, then sign in with your QuickBooks Online email or user ID and password. After that, click Authorize to give ShipStation access.
STEP 3
Back in ShipStation, click Manage Settings and choose your transaction type. If you select Sales Receipts, map assets and income accounts. If you select Invoices, map the income account.
STEP 4
Choose which stores submit shipped orders, decide whether to export customer information and sales tax, then process transactions by date range or enable the Automatic option from the Process Orders tab.
TESTIMONIAL
Find the best rate for every shipment
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ShipStation AI
Next-gen shipping intelligence
- SmartFill
- Automated Order Creation
- Universal AI Connect (MCP)
- Batch Label Processing
- Auto-PRO Retrieval
- Dynamic Spot-Pricing Engine
- Packing Recommendations
- 24/7 Always-On
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FAQ
QuickBooks Online and ShipStation FAQ for invoices, orders, inventory, and reports
Does shipping write back to the QuickBooks Online invoice automatically?
No. The direct QuickBooks Online integration is built to send shipped order data from ShipStation into QuickBooks Online so it appears there as either sales receipts or invoices. You can send that data manually, or turn on the Automatic option from the Process Orders tab. The workflow focuses on creating QuickBooks Online records for shipped orders, not editing an existing invoice line by line after shipping happens. If your team expects true invoice write-back, set expectations around record creation first.
Does ShipStation work with both QuickBooks Online and QuickBooks Desktop?
No. ShipStation’s direct connection is for US-based QuickBooks Online accounts only. ShipStation does not support QuickBooks Online Canada. For other QuickBooks versions, ShipStation points users to a third-party connector. That means the direct ShipStation integration with QuickBooks Online is the right fit when your accounting workflow already lives in US-based QuickBooks Online, not desktop.
If I create an order in QuickBooks, does it sync to ShipStation?
No. The documented data flow goes from ShipStation to QuickBooks Online for orders that are already in Shipped status. The setup, features, and processing steps do not include importing orders created inside QuickBooks Online into ShipStation. In most shipping workflows, orders come from your connected store or marketplace, ShipStation handles fulfillment, and QuickBooks Online receives the shipped order record after the shipment is done. That direction matters, because it tells your team where order creation should start.
Does ShipStation connect to my inventory through QuickBooks or through my store?
No. The direct QuickBooks Online connection is built for accounting output, not for bringing order flow into ShipStation from QuickBooks Online. ShipStation sends shipped order, product, customer, and sales tax data into QuickBooks Online, while fulfillment usually starts with the stores and channels you connect for orders. That gives you a cleaner split: your selling channels drive operational order details, and QuickBooks Online keeps the financial record of what shipped. When teams mix those roles, reconciliation gets harder.
Will it handle kits and assemblies the way a build assembly does in QuickBooks?
No. The direct QuickBooks Online integration maps products by SKU or creates new non-inventory product records in QuickBooks Online when needed. It does not describe build assembly support, assembly logic, or Desktop-style manufacturing behavior. If your business depends on kits, assemblies, or a build assembly workflow, treat that as a separate validation point before rollout. **Tip:** Review how your SKUs post into QuickBooks Online first, because that’s how the direct integration handles products.
Can I export shipping reports into QuickBooks?
No. The documented QuickBooks Online integration is built to send shipped order data into QuickBooks Online as sales receipts or invoices. It does not include a feature for exporting ShipStation shipping reports into QuickBooks. What you do get is a posting flow for shipped orders, plus the choice to send that information manually or automatically. If month-end shipping spend review is important, plan around shipped order records in QuickBooks Online rather than expecting ShipStation report exports to land there.
Which system should be the source of truth when my store and QuickBooks disagree?
Use your selling channel as the source of truth for order details that feed fulfillment, and use QuickBooks Online as the source of truth for the accounting records ShipStation creates after orders ship. That approach matches how the integration works. ShipStation fulfills the operational side, then sends shipped order data into QuickBooks Online. When something looks off, check it in this order:
- Review the original order in the connected store or marketplace
- Confirm what shipped in ShipStation
- Check the QuickBooks Online record created from that shipped order
That sequence usually shows where the mismatch started and keeps your team from fixing the wrong system first.
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