Shopify QuickBooks Integration: How to Connect Them and Which Connector to Use

Shopify connects to QuickBooks Online through an Intuit-built app

Shopify integrates with QuickBooks Online through the QuickBooks Online app in the Shopify App Store, which is built by Intuit and marked free to install. Intuit says the connector is included with a QuickBooks subscription. The alternative is a third-party connector such as Link My Books, A2X, Taxomate, Synder or Bold QuickBooks Sync Pro.

You need a QuickBooks Online plan first: Simple Start, Essentials, Plus or Advanced. Intuit's US pricing page showed promotional pricing on 3 October 2026, so this page quotes no QuickBooks price; check the current price on Intuit's site.

What the Intuit connector syncs from Shopify

• Sales, payments and payouts, with sales, taxes, fees and shipping mapped to categories for you.
• Products and inventory: products are matched to QuickBooks inventory so quantities and costs stay aligned.
• B2B orders as invoices, with customer details and payment terms.
• History: Intuit says it reconciles up to 12 months of sales history.

The Shopify App Store listing showed a 4.6 rating from 3,327 reviews on 3 October 2026. It is worth reading the newest reviews before you rely on it: three dated October 1 and 2, 2026 describe problems after a recent connector update, including sales tax fields left empty and orders posted under a generic customer. Those are individual merchant reports, not a measured defect rate. Inventory tracking in QuickBooks Online itself starts at the Plus plan.

Six ways to connect Shopify to QuickBooks Online, with prices

Link My Books has lower tiers below 200 orders, from $20 a month for up to 15 orders. Link My Books' Shopify App Store listing showed lower prices than linkmybooks.com on the same date, $21 against $24 for Starter 200 Lite, so this page uses the linkmybooks.com figures and you should confirm the price at signup.

Order-level sync or payout summaries: how to choose

The options split into two methods. Order-level tools copy each Shopify order into QuickBooks. Payout tools post one journal per payout, so the ledger stays small and each entry equals a bank deposit. Sales totals versus payout totals explains why the two give different pictures.

• You want inventory quantities and B2B invoices in QuickBooks: the Intuit connector. Taxomate states that its Shopify workflow does not sync inventory.
• You want each bank deposit explained with the fewest entries: a payout connector such as Link My Books, A2X or Taxomate.
• You take PayPal, Klarna or other gateways: Link My Books documents support for every Shopify gateway, with a clearing account for each.
• You want per-order records without the Intuit connector: Synder in per-transaction mode, or Bold.

Where Link My Books fits, and how to connect it

Link My Books fits a Shopify store that wants journal entries at payout level and also sells on other channels. It does not sync inventory or individual orders. Prerequisites: QuickBooks Online, not Desktop or Self-Employed, and a Link My Books plan sized to your orders. The documented steps are:

1. Start the 14-day trial by signing in with your QuickBooks account. The vendor says no card is needed.
2. Connect your Shopify store. The vendor says it needs read-only access.
3. Confirm the suggested accounts and tax rates, and assign the QuickBooks bank account for deposits.
4. Turn on auto-post and set the date from which it should post.
5. Match each Shopify deposit to its journal in QuickBooks banking.

Worked example: a store with 800 orders a month would be on 1K Lite at $47 a month on linkmybooks.com, on top of its QuickBooks Online subscription. A mistake to avoid, from the Link My Books documentation: rolling back a settlement removes the journal it posted, and the rollback fails if QuickBooks has already matched that journal in a different account. The documented fix is to delete the journal yourself, which is permanent, so check that you have the right entry first. More detail is in Link My Books for Shopify and the Link My Books QuickBooks integration page.