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

Connect Shopify and QuickBooks Online through QuickSync to sync eligible Inventory item quantities and sales. Eligible new fully paid sales export as Sales Receipts; unpaid or partially paid sales export as Invoices. Sales syncing requires Pro or higher. Existing bound documents keep their type.

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14-day trial · no credit card · sales syncing requires Pro or higher

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How to connect Shopify and QuickBooks

  1. 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

  2. Connect QuickBooks

    You sign in to Intuit and pick the company file. QuickSync writes to that company and nothing else.

    ~1 minute

  3. Choose what to sync

    Pick all products or a list, the source store and its locations. Existing products match by SKU.

    ~5 minutes

  4. 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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14-day trial · no credit card · sales syncing requires Pro or higher

Step by stepHow to connect ShopifyTurn on Track quantity in ShopifyHow to connect QuickBooksQuickSync setup guideCheck your SKUs before syncingAll docs

Choose how you keep Shopify and QuickBooks in sync

RouteWhat it syncsWhat it costsLimits 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 a sales document per order or move the quantity on an item. Set up from inside QuickBooks Online.
A2X, Synder or another payout appEach 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 RecommendedAutomatic Shopify sales sync: Sales Receipts for fully paid sales; Invoices for unpaid or partially paid sales. Inventory quantities sync separately for eligible items.Sales syncing requires Pro or higher. 14-day trial, no credit card. See the pricing page.Nothing comes back out of QuickBooks, by design
Third-party prices and limits as each vendor publishes them; ours from our pricing page. Checked 17 October 2026.

What QuickSync syncs between Shopify and QuickBooks

WhatShopifyQuickBooks
Stock countBoth waysBoth ways, as a book figure
New listingsWe can create and updateNot a storefront, so no listings
PricesSent, with your rule appliedWritten to the item
Orders inInto QuickSyncSales Receipts or Invoices go in; no sales-order import
Tracking backSent to the orderNot applicable
Photos and optionsPhotos, sizes and coloursNot a storefront, so no photos

Example: follow one Shopify sale

For sellers who use Shopify and QuickBooks Online. Match items by SKU, choose inventory and sales syncing separately, and check the payment state of each sale before export. Cancellation handling depends on the document and verified payment state. Paid, partially paid or refunded documents are retained for reconciliation; cancellation alone doesn’t authorize a refund. Eligible new fully paid sales export as Sales Receipts; unpaid or partially paid sales export as Invoices. Sales syncing requires Pro or higher. Existing bound documents keep their type.

Shopify Shopify · order #447114:02:11
Classic Tee, Black, M1 × $24.00
Stock before this sale42
Synced automatically
Shopify and QuickBooks QuickBooks sale synced
ChannelFigureUpdated
ShopifyShopify41sold here
Shopify and QuickBooksQuickBooks41updated

What to know before you connect

Inventory limit

QuickBooks is your books, not a shop

QuickBooks Online must support inventory tracking for quantity sync on linked Inventory items. Eligible sales sync as Sales Receipts or Invoices on Pro or higher; sales orders are not imported back into your shops.

Automatic after setup

Choose your settings once. QuickSync handles the sync.

Turn on inventory syncing for linked Inventory items. Enable eligible sales syncing on Pro or higher to send paid sales as Sales Receipts and unpaid or partially paid sales as Invoices. QuickSync then syncs automatically; you do not retype each sale.

4:12pm

Nothing waits here

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

Shopify announces new orders through webhooks. QuickSync checks each sale’s payment state, mapping and export eligibility before sending it to QuickBooks Online. Processing time also depends on queues and QuickBooks API responses.

Use this connection when Shopify and another shop share the same inventory. Eligible item quantities can sync across those connected stores; bank deposits and payout reconciliation remain separate.

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 a sales document 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.

Cancellation handling depends on the document and verified payment state. Paid, partially paid or refunded documents are retained for reconciliation; cancellation alone doesn’t authorize a refund. 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 GuideHow to Sync Shopify and QuickBooks Online InventoryBest Shopify QuickBooks Integration Apps (2026 Compared)

Questions people ask about this pair

Do my Shopify products show up as listings in QuickBooks?

No. QuickBooks Online is an accounting system, not a storefront. QuickSync links items by SKU and can sync quantities for eligible Inventory items. Sales syncing on Pro or higher sends fully paid sales as Sales Receipts and unpaid or partially paid sales 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 sales document after eligibility checks 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. A sales document 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 sales document when a Shopify order is cancelled?

Cancellation handling depends on the document and verified payment state. Paid, partially paid or refunded documents are retained for reconciliation; cancellation alone doesn’t authorize a refund.

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?

Supported shipment updates return to the original order when the connected fulfillment store supplies them. Supported tracking details can return to the originating Shopify order. QuickSync does not push carrier or tracking numbers to QuickBooks.

Do orders flow both ways with QuickBooks?

No. Eligible sales from Shopify sync into QuickBooks when it is your fulfillment store and order syncing is enabled on Pro or higher. Fully paid sales become Sales Receipts; unpaid or partially paid sales become Invoices. Sales orders are not imported back out of QuickBooks into your shops.

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 supports inventory syncing for eligible items. Sales syncing into QuickBooks Online requires Pro or higher. Your QuickBooks Online plan must support inventory tracking for quantity sync. Start with a 14-day trial, with no credit card, and check our pricing page for current plans.

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