Shopify QuickBooks integration that keeps your books in step with your stock

Yes. QuickSync writes each Shopify order into QuickBooks as its own invoice the second it’s placed and sets the quantity on hand on the matching item, so the books describe the shelf on the day, not the payout a week later.

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How to connect Shopify and QuickBooks

Connect Shopify
You connect your shop from QuickSync and approve it in your Shopify admin. Shopify asks which permissions to grant and you can withdraw them from the Shopify side at any time.
~1 minute
Connect QuickBooks
You sign in to Intuit and pick the company file. QuickSync writes to that company and nothing else.
~1 minute
Choose what to sync
Pick all products or a list, the source store and its locations. Existing products match by SKU.
~5 minutes
Start syncing
Click Start Syncing. Stock aligns from your source store, then stays in step on its own.
Depends on catalogue size

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Step by stepHow to connect Shopify Shopify FAQs How to connect QuickBooks QuickBooks FAQs QuickSync setup guide Check your SKUs before syncing All docs

Choose how you keep Shopify and QuickBooks in sync

Third-party prices and limits as each vendor publishes them; ours from our pricing page. Checked 7 October 2026.
Route	What it syncs	What it costs	Limits and exceptions
QuickBooks Connector for Shopify (Intuit)	Sales, refunds and processing fees, grouped by payout, into a review tab to match against the bank feed.	Free.	Payout-level: it doesn’t write an invoice per order or move the quantity on an item. Set up from inside QuickBooks Online.
A2X, Synder or another payout app	Each payout split into sales, fees, refunds and tax, to the penny.	From about $20 a month, varies by app.	Books only. A payout total can’t move the count on one item, and nothing here keeps a second shop level.
QuickSync Recommended	Each Shopify sale as its own invoice, and the quantity on hand on the matching QuickBooks item	$19 a month for two shops on Lite, after a 14-day trial with no card	Nothing comes back out of QuickBooks, by design

What QuickSync syncs between Shopify and QuickBooks

What	Shopify	QuickBooks
Stock count	Both ways	Both ways, as a book figure
New listings	We can create and update	Not a storefront, so no listings
Prices	Sent, with your rule applied	Written to the item
Orders in	Into QuickSync	Invoices go in, nothing comes back
Tracking back	Sent to the order	Not applicable
Photos and options	Photos, sizes and colours	Not a storefront, so no photos

Follow one Shopify sale

Say a Shopify order for three of one product lands at 4:12pm. On QuickBooks’ own connector, that sale reaches the books as part of the payout it belongs to, grouped with fees and refunds, days later when Shopify pays out. On QuickSync, at 4:12pm an invoice for that order is in the company file and the item’s quantity on hand has dropped by three. Both are correct. They answer different questions, and this page is about telling them apart before you pick one.

Shopify · order #447114:02:11

Classic Tee, Black, M1 × $24.00

Stock before this sale42

Synced automatically

QuickBooks invoice written

ChannelFigureUpdated

Shopify41sold here

QuickBooks41updated

What to know before you connect

Inventory limit

QuickBooks is your books, not a shop

Quantities in QuickBooks are a bookkeeping figure no shopper ever sees, and orders go in as invoices without coming back out. That is by design, not a gap.

Manual control

Stock moves when you say so

QuickBooks is not a storefront, so there is no listing to publish. Stock and invoices move once you turn sync on; nothing invents a product page on Shopify.

4:12pm

Nothing waits here

Shopify announces the order. QuickBooks accepts the write. No timer sits between them.

Shopify tells us about an order the moment it’s placed, and writing to QuickBooks takes under a second from there. That makes this one of the quieter pairs to run: no interval to sit behind, no gap between the sale and the entry. Compare a marketplace pair, where an Etsy order is looked for every five minutes and a busy hour can put a few sales a step behind.

Where the same-second write pays off is the second shop. Most people asking this question run Shopify and something else, an Etsy shop, an Amazon listing, a Square till, and the QuickBooks item is the one place all of them meet. If the quantity there is set from every shop as each sells, the books describe the shelf. If it’s set from one shop’s payout every few days, they describe the past.

If reconciling is the whole job

What a sale writes, and when the free connector is enough

Payout apps do the books from the deposit. We write the sale. Different questions, and some sellers run one of each.

We start from the order. A Shopify sale becomes an invoice in the company file you picked when you connected, in the order’s currency, with the customer matched by name or email, and we set the quantity on hand on the matching QuickBooks item. Change a price in Shopify and we write it onto the item too, so margin reports in QuickBooks stop drifting from what the shop charges. The SKU is how items pair: Shopify holds 255 characters, QuickBooks 100, so anything longer is cut to fit, and the two stop matching without an error. Give both the same SKU under 100 characters.

A payout app starts from the money that reached your bank. Shopify pays out every few days; the app takes that deposit, splits it into sales, fees, refunds and tax, and posts one entry that matches the bank line to the penny. That’s what an accountant wants at month end, and QuickBooks Connector for Shopify (Intuit’s own, free, set up from inside QuickBooks Online) does a plain version of it. Intuit’s listing has the current details. If that’s your whole job, use it and stop reading.

Cancel the order in Shopify and the invoice is voided. Nothing ever comes back out of QuickBooks: it’s your books, not a shop, so there’s no listing to create, no order to import from it, and no tracking number to send it. The quantity we set there is a figure for your reporting and your accountant, not a count a customer can buy from.

Connecting

Two approvals

Approve QuickSync in Shopify, sign in to Intuit, pick the company file.

Connect your shop from QuickSync and approve it in your Shopify admin; Shopify shows the permissions and you can withdraw them from its side at any time. Then sign in to Intuit and choose the company file. We write to that company and nothing else. Match products by SKU, decide which shop holds the true count on day one, and turn the sync on. Nothing is written to a live shop until you’ve looked at the match.

Guides for running Shopify and QuickBooks together

How to Reconcile Shopify in QuickBooks: Payout Guide How to Sync Shopify and QuickBooks Online Inventory

Questions people ask about this pair

Do my Shopify products show up as listings in QuickBooks?

No. QuickBooks is your books, not a storefront, so there is nothing to list. We write the item and the quantity as a bookkeeping figure, and orders arrive as invoices.

Does Shopify integrate with QuickBooks?

Yes, two ways. Intuit publishes a free QuickBooks Connector for Shopify that brings sales, refunds and fees into QuickBooks Online grouped by payout, for reconciling against the bank feed. A sync app such as QuickSync writes each Shopify order as its own invoice the moment it’s placed and sets the quantity on hand on the matching item.

How do I connect QuickBooks to Shopify?

For Intuit’s connector: open Integrations inside QuickBooks Online, find the Shopify connector and authorise your store. For QuickSync: start a trial, connect your shop and approve it in Shopify, sign in to Intuit, pick the company file, then match products by SKU. Keep SKUs under 100 characters, QuickBooks’ limit.

What’s the best Shopify QuickBooks integration?

It depends on the job. Reconciling payouts to the penny: A2X or Synder, or Intuit’s free connector if your volume is modest. An invoice per sale with item quantities kept true across Shopify and your other shops: a sync app. Many sellers run one of each, because they answer different questions.

Does the QuickBooks integration sync inventory with Shopify?

QuickSync sets the quantity on hand on the QuickBooks item as Shopify sells, and as any other connected shop sells. It’s a bookkeeping figure: no customer buys from QuickBooks, so nothing flows back out of it into Shopify.

What happens to the invoice when a Shopify order is cancelled?

The invoice is voided in QuickBooks and the item quantity is corrected. Refund handling and payout reconciliation stay with your accountant or a payout app; we don’t post to bank or clearing accounts.

How long can a SKU be for Shopify and QuickBooks?

One hundred characters. Shopify allows 255; anything longer is cut to 100 on the way to QuickBooks and stops matching the item. Use the same SKU under 100 characters in both.

Do prices sync from Shopify to QuickBooks?

One way, yes. The price you set on Shopify is written to the matching item in QuickBooks, so the books read what you actually charge. QuickBooks never writes a price back, so that number stays yours to set on Shopify.

Does the tracking number go back to Shopify?

Yes, to Shopify. When you add a tracking number to an order we send it back and the buyer gets the shop’s normal notification. QuickBooks holds the invoice rather than the buyer, so there is nobody there to notify.

Do orders flow both ways with QuickBooks?

No. A Shopify sale becomes an invoice in QuickBooks. Nothing is imported back out of QuickBooks into your shops; it is a one-way accounting sink by design.

What happens if I refund a Shopify order?

When Shopify reports an actual restock, the inventory quantity can sync to the books. A refund alone does not restore stock. Handle invoice credits in QuickBooks separately.

Which plan do I need for Shopify and QuickBooks?

Lite covers Shopify and QuickBooks. Lite is $19 a month for two shops and holds 1,000 items, with up to eight connected integrations. You would move up a plan for catalogue size, and your bill goes up by another $19 if you connect a third shop.