Shopify QuickBooks Integration Compared

There are three ways to get Shopify sales into QuickBooks Online: Intuit's own Shopify app, a payout connector such as A2X or Link My Books, or Nummbas, which splits each payout and sends it to QuickBooks as a summary. The right choice depends on how much detail you want in QuickBooks and how much matching you want to do by hand.

Nummbas is our pick for most stores. It sends one clear entry per payout, covers Stripe, Square, eBay, Amazon and TikTok Shop (US) payouts as well as Shopify Payments, and gives you the option to move your books into Nummbas Books later.

Option 1: Intuit's Shopify app for QuickBooks Online

Intuit's Shopify connector is free to install and included with every QuickBooks Online plan. According to Intuit's help article, it records:

• Each order as a sales receipt, or as an invoice for B2B orders
• Shopify fees as expenses
• Each payout as a deposit for the net amount, which you then match to the bank line
• Refunds one by one, with their tax and products

It can import transactions from up to 12 months back. Products are matched to QuickBooks items by SKU and name. A product with no match is not added for you, so its sales go to a default Shopify sales item until you create it.

Intuit also notes that some payout adjustments need you to choose an account before the payout can be added, and that you should match the deposit rather than add it from the bank feed, or it will be counted twice.

Best suited to: stores with lower order volumes that want every order in QuickBooks. At higher volumes, one entry per order means thousands of transactions to review each month.

Option 2: a payout connector

A payout connector reads each Shopify payout and posts it to QuickBooks as a summary, split into sales, refunds, fees and tax, so the entry equals the bank deposit.

Prices are list prices with monthly billing as of November 2026. A2X has announced higher prices for its plans above Mini from 14 November 2026. Every connector is paid on top of your QuickBooks plan, and its price rises with your order count.

Best suited to: stores that want summarised entries and are happy to pay for a second subscription that grows with their orders.

Option 3: Nummbas with QuickBooks Online

Nummbas reads payouts from Shopify Payments, Stripe, Square, eBay, Amazon and TikTok Shop (US) and sends each one to QuickBooks Online as a summary. Set it up in three places:

1. Payout summaries lists each payout split into sales, fees, refunds and tax. A payout that crosses a month end gets a part for each month.
2. Accounts to use is where you choose the QuickBooks account for each part.
3. Sending is where you turn sending on. Nothing is sent until you do.

With inventory management, you can also turn on Stock and cost of goods, which sends each month's stock and cost of goods to QuickBooks as one entry.

Best suited to: stores that sell through more than Shopify Payments, want one entry per payout and want profit and stock insight in the same product.

Or skip the integration: keep your books in Nummbas Books

If you are choosing QuickBooks only to record store sales, Nummbas Books does that work without a connection to maintain. It splits each payout, links it to the bank deposit, records invoices, bills and receipts, prepares sales tax returns and closes the month with you or your accountant.

How to set up any Shopify QuickBooks integration

1. Use one connection only. Two apps posting the same sales doubles your income. Turn off any older sync before you start.
2. Choose a start date. Pick the first day of a month after your last reconciled month, so the new entries do not overlap old ones.
3. Map the accounts. Decide where sales, shipping income, refunds, fees and sales tax go before anything is posted. Sales tax belongs in a liability account, not income.
4. Test one payout. Take one closed payout, check the entry against Shopify's payout report and match it to the bank deposit.
5. Review the first month. Compare sales, refunds and fees for the month with Shopify's reports before you trust the setup.

Shopify QuickBooks integration FAQs

Does Shopify integrate with QuickBooks?

Yes. Intuit publishes a free Shopify app for QuickBooks Online that records each order, fee and payout. You can also use a payout connector or Nummbas, which send each payout to QuickBooks as a summary.

Is the QuickBooks Shopify app free?

It is free to install and included with your QuickBooks Online subscription, which starts at $38 a month. Inventory tracking in QuickBooks starts on the Plus plan at $140 a month.

Should I send each order or a summary to QuickBooks?

A summary per payout keeps QuickBooks easy to reconcile, because each entry equals a bank deposit. Each order gives more detail but creates many more transactions to review. Order and product detail is available in Nummbas without adding it to your ledger.

Can I use two Shopify QuickBooks integrations at once?

No. Two connections posting the same sales count your income twice. Choose one and turn the others off.

Do I need QuickBooks if I use Nummbas?

No. Nummbas Books records your sales, payouts, bills and bank transactions in its own books. Keep QuickBooks if your accountant prefers it, and Nummbas will send each payout there as a summary.