Shopify QuickBooks integration that keeps stock, prices and books in step.

Yes. Intuit publishes a connector for QuickBooks Online, listed on the Shopify App Store as QuickBooks Online. It brings Shopify sales, refunds, fees, taxes and payouts into your books. QuickBooks Desktop and Enterprise connect through a separate QuickBooks Desktop Connector app or a third-party tool. Which route fits depends on your QuickBooks version and on which system holds your stock and prices.

Intuit's help article lists what you need: a QuickBooks Online account, your original myshopify.com store address, your Shopify login, and permission to install apps in Shopify. You then open the Shopify Connector by QuickBooks inside QuickBooks Online and follow the prompts. Intuit says the first import takes between 10 minutes and 3 hours, depending on how many transactions there are.

It depends on which system leads. If Shopify is where sales happen and QuickBooks only needs correct totals, Intuit's own connector is free to install and rated 4.6 out of 5 from 3,330 reviews on the Shopify App Store. If QuickBooks holds your stock and prices, look for an app that documents sending them to Shopify. MyWorks lists that on its support page.

For sales flowing into the books, yes. Intuit's connector records each sale as a Sales Receipt and its fee as an Expense, and it tracks the sales tax Shopify collected. The other direction is harder. Intuit's help article does not describe QuickBooks sending stock counts or prices to Shopify, so stores that need that add a second tool or a custom sync.

The Shopify App Store listing says it is free to install and that additional charges may apply. The same listing says the connector is included with a QuickBooks subscription, and that external charges may be billed by Intuit separately from your Shopify invoice. You still pay for QuickBooks Online itself.

No. Shopify records your orders, your payouts and the tax it collected, and it has sales reports. It is not accounting software. It does not keep a general ledger, which is the full record of money in and out that your accountant works from. That is why stores connect Shopify to QuickBooks.

Yes. The Shopify App Store lists a QuickBooks Desktop Connector, made by a company called LINK. Shopify's help center says it works with QuickBooks Desktop versions 2021 to 2024 and syncs once a day at a time you choose. Shopify wrote that guide for merchants moving from QuickBooks Desktop POS to Shopify POS, so check that it fits your setup before relying on it.

Yes. Shopify lists QuickBooks Desktop Enterprise (Subscription) as compatible with the QuickBooks Desktop Connector. Third-party tools cover it as well: Webgility says it syncs Shopify with QuickBooks Online or Desktop. When Enterprise holds stock across several sites or price levels by customer, a custom sync is often the cleaner route.

Partly. Intuit stopped selling new subscriptions of QuickBooks Desktop Pro Plus, Premier Plus and Mac Plus to US customers after September 30, 2024. Existing subscribers can keep renewing, and Intuit says it will keep providing security updates and support for them. QuickBooks Desktop Enterprise is still sold to new customers.

Plus or Advanced. Intuit's help page says that with QuickBooks Online Plus or Advanced you can track how much of each product you have in stock. An inventory item there holds a name, a SKU, a quantity on hand, a reorder point, a sales price and a purchase cost. Those are the fields a Shopify sync reads.

Once a day, at a time you pick, with a manual sync available whenever you want one. Shopify's help center says this changed on November 7, 2023. Before that date the connector synced every 5 minutes.

Yes, with the right tool. Intuit's own connector is documented as moving sales into QuickBooks. Sending stock counts the other way takes a two-way connector app or a custom sync. Shopify allows it: its developer documentation has a command that sets stock quantities to an exact number, and that is what a sync uses.

Yes. A master is the one copy everyone trusts. If your price list is kept in QuickBooks, a sync can send each change to Shopify so nobody retypes it. MyWorks documents product prices syncing in both directions between QuickBooks Online and Shopify. For price levels by customer, or rules an app cannot follow, we build the sync.

With Intuit's connector, each sale arrives as a Payment Received transaction. When you confirm it, QuickBooks Online creates a Sales Receipt for the sale and an Expense for the fee. Wholesale orders are imported as invoices. Other tools work differently: A2X posts one summary for each Shopify payout.

A payout is the bank transfer Shopify sends you. Intuit describes it as typically covering sales over a one-day period, with several sales and adjustments inside. It arrives with fees and refunds already taken out, so it will not equal any single order. A good setup records the sales, fees and refunds behind each payout so the deposit can be matched.

Intuit's connector imports transactions from up to one year ago. Anything older needs a different method, which we scope case by case.

Intuit's connector does. Shopify B2B and wholesale orders are imported into QuickBooks as invoices. When a customer pays outside the store and you mark the invoice paid in QuickBooks, that status is sent back and the order is marked paid in Shopify. Payment terms and customer price lists need checking case by case.

Intuit's connector tries to match products by SKU and name with the ones already in QuickBooks Online, to avoid duplicates. A product it cannot match has to be matched or created by hand on the review screen. That is why we clean the item list before connecting anything.

It depends on the route. Intuit's connector is free to install with a QuickBooks subscription. The QuickBooks Desktop Connector lists a free plan and a B2B plan at $99 a month. For custom work, Shopify developers in the US and Canada typically charge $120 to $200 an hour, according to CartCoders' 2026 rate guide. FactoryJet quotes a fixed price in writing after a short scoping call.

Turning on Intuit's connector is a same-day job: Intuit says the first import takes between 10 minutes and 3 hours. A custom sync is a project, so plan time for cleaning the item list and for testing. The timeline goes in writing with the quote.

No. Your bookkeeper or accountant decides how sales, fees and tax should post. We are engineers. We make Shopify and QuickBooks follow those decisions, and we keep the connection running. We are happy to work with them directly.

Yes. Before a contract, we show working software on your own data. For this kind of project that means a sample of your own items moving between a test store and QuickBooks, so you can check the entries it creates.

Any business that sells stock and keeps its books in QuickBooks: distributors, manufacturers, retailers with a shop and a website, food and drink makers, and consumer brands. FactoryJet was founded in 2014 and has served more than 500 businesses.

No. FactoryJet is a registered Shopify Partner, without a Plus Partner tier. We do the engineering work itself. If your procurement team requires a Plus Partner badge, tell us on the first call.