How Does the QuickBooks Online Shopify Connector Import Invoices?

The QuickBooks Shopify Connector now imports B2B (wholesale) Shopify orders directly as invoices, with company details, PO numbers, and payment terms already filled in. It does this by routing every Shopify order into the Integration Transactions tab, where B2B orders post as linked invoices and DTC (retail) orders post as sales receipts. For merchants running both retail and wholesale through Shopify, that means less manual data entry and one less spreadsheet to reconcile at month-end.

What changed with Shopify invoice import in 2026?

Two things changed: the connector itself, and how it treats B2B orders. Earlier in 2026, we retired the legacy Shopify integration (the one some merchants knew as OneSaaS or "Connect to Shopify") and moved every store to the rebuilt Shopify Connector by QuickBooks, which holds incoming transactions in a For Review queue instead of posting them straight to your books. Then in June 2026, as part of Shopify Editions, we added native B2B support: wholesale orders now import automatically as invoices instead of needing manual entry.

If you only sell direct-to-consumer (DTC), the day-to-day hasn't changed much beyond the review-queue step. If you sell wholesale too, invoice import is the bigger shift, and it's the focus of the rest of this guide. (Separately, a September 2026 update added two-way inventory sync between Shopify and QuickBooks. Worth knowing about, but it's a different workflow than invoicing.)

How does invoice import work for B2B Shopify orders now?

The direct answer: when a B2B order is placed in Shopify, QuickBooks creates an invoice automatically, with the order's company and payment details already attached, you don't build it from scratch.

What gets imported onto the invoice

• Order details: products, services, quantities, rates, taxes, and discounts
• Company profile: company name, billing address, email, phone, and website (B2B orders attach this info to a Company instead of an individual customer)
• Payment terms: terms like Net 30 or Net 60 come in from the Shopify order and apply directly to the invoice
• Identification tags: the Shopify order number and PO number, so you can trace an invoice back to its source order
• Customer segmentation: Shopify B2B companies import as Customers and get tagged "Shopify B2B company" automatically, so they're easy to filter in reports

What happens when a B2B invoice gets paid

If a wholesale order is paid through Shopify, QuickBooks creates an Invoice Payment and links it to the matching invoice automatically. If the invoice hasn't been confirmed yet,it's still sitting in the For Review tab. You'll see "No invoice found" instead; confirming the invoice (or manually selecting it) resolves that. The sync also runs in reverse: mark the invoice paid in QuickBooks (say, you got paid by wire outside Shopify), and that paid status pushes back to Shopify so both platforms agree on order status.

(Good spot for a screenshot of the Integration Transactions tab showing a B2B order mid-review filename: quickbooks-shopify-b2b-invoice-review-queue.png, alt text: "QuickBooks Online Integration Transactions tab showing a Shopify B2B order imported as an invoice.")

How do DTC and B2B Shopify orders differ once they hit QuickBooks?

They don't land the same way, and mixing up the two is the most common source of confusion we hear about. Here's the side-by-side:

Both order types ultimately flow into the same payout and deposit, so your bank-matching step at the end stays the same either way.

How do you review and confirm Shopify invoices without stalling your books?

Short answer: work the For Review queue before you touch Bank Transactions, in this order:

1. Go to Integration Transactions (All apps → Accounting → Integration Transactions). This is where every Shopify order, invoice, and payout lands first.
2. Confirm what's ready. Anything marked "Confirm" has complete information. Company, product, payment terms and posts in one click.
3. Fix what's flagged "Review." Missing a product match or company detail? Fill it in, then confirm. Until you do, the invoice won't hit your reports.
4. Add the payout once every included transaction is Categorized. This creates the Deposit transaction, which bundles together the confirmed Sales Receipts, Receive Payments (for B2B orders), and Expenses from Step 2–3.
5. Match, don't add, in Bank Transactions. QuickBooks suggests a match between the bank deposit and the Deposit you just confirmed. Select Match; don't manually re-create the deposit, or you'll double it up.

Skipping straight to Bank Transactions before confirming everything upstream is the single most common cause of an invoice that "disappears".  It's not gone, it's still waiting in For Review.

What should you do if a Shopify invoice doesn't show up or looks wrong?

Start in the For Review tab, not the Bank Feed. Most "missing invoice" reports come down to one of three things: the order is still sitting in Review waiting on a product or company match, the payment arrived before the invoice was confirmed (hence "No invoice found"), or the order was accidentally excluded. Check the Excluded tab too, transactions only land there if someone excluded them manually, so if an invoice seems to have vanished, that's worth a look before assuming it's a sync failure. If none of that explains it, QuickBooks Support can see the sync logs on their end; use the chat icon on the Shopify app tile or email qbo-integrationsupport@intuit.com.

FAQ

Why did my Shopify wholesale orders start showing up as invoices instead of sales receipts?

That's the June 2026 B2B update. Before that, every Shopify order, retail or wholesale, synced the same way. Now B2B orders specifically generate an Invoice tied to a Company profile, with payment terms and PO numbers already filled in.

What happened to the old Shopify connector app?

It was retired in 2026. If you were on the legacy app (sometimes called OneSaaS or "Connect to Shopify"), you were migrated to the rebuilt Shopify Connector by QuickBooks, which reviews transactions before posting instead of syncing them instantly.

Do I need to manually enter payment terms and PO numbers for B2B orders?

No. Both come in automatically from the Shopify order and apply directly to the invoice, there's nothing to retype.

What does "No invoice found" mean when a Shopify payment comes in?

It means the matching invoice hasn't been confirmed yet and is still in the For Review tab. Confirm the invoice first, or select "Select a different invoice" to link it manually.

Can I still handle a B2B order manually instead of letting it auto-generate an invoice?

There's no separate toggle to turn off invoice automation for B2B orders. If one needs different treatment, you can exclude it from the For Review tab and create the invoice yourself instead.

If I mark an invoice paid in QuickBooks, will Shopify know?

Yes. Payment status syncs both directions. Mark it paid in QuickBooks and the order updates to paid in Shopify too.

Key Takeaways

• Earlier in 2026, Intuit retired the legacy Shopify connector; every store now runs on the Shopify Connector by QuickBooks, which reviews transactions before posting them.
• June 2026 added native B2B support: wholesale orders auto-import as invoices with company, PO, and payment-terms data already attached.
• DTC orders still post as sales receipts: only B2B orders generate invoices.
• Confirm everything in Integration Transactions before you ever touch Bank Transactions; match deposits, don't recreate them.
• Paid status syncs both ways between QuickBooks and Shopify automatically.

Still stuck on a Shopify invoice?

Drop the specifics in the comments such as what the order looked like, which tab it's stuck in, and we'll help you track it down. If it's affecting your books right now, use the chat icon on the Shopify app tile in Integration Transactions, or email qbo-integrationsupport@intuit.com. And if the hang-up is really on the banking side, this guide to avoiding bank connection errors is a good next stop.

Helpful Resources

• Connect Shopify to QuickBooks Online: full setup steps, settings glossary, and the complete B2B invoice/payment mechanics.
• Migrate to the new QuickBooks Online e-commerce connectors: what to do if you're still on a legacy connector (Shopify, Amazon, eBay, Etsy, and more).
• QuickBooks adds native B2B support for Shopify merchants: the official announcement behind the June 2026 invoice automation.
• What's new in QuickBooks Online: September 2026: covers the related two-way inventory sync update.