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Shopify + QuickBooks

Shopify + QuickBooks reporting,from the order to what landed in the bank.

Ask what each product made after fees, refunds and its real cost, or which payouts never made it into the books. Querri copies your Shopify store and your QuickBooks Online company into one Library on a schedule and lines the two up for you.

Querri only reads from Shopify and QuickBooks and never changes an order, a product or an entry. You approve access on Shopify's screen and Intuit's, so Querri never sees a password. SOC 2 Type II, HIPAA and ISO 27001:2022 certified.

Why Shopify + QuickBooks reporting gets hard

Shopify records the sale. QuickBooks records what's left of it.

Owners, bookkeepers and fractional CFOs all run into the same gap at month-end. The store says one number, the bank says another, and the days in between go to a spreadsheet that ties them together by hand.

01

A payout is never the order total

Processing fees come out before Shopify Payments sends a payout, and disputed amounts, dispute fees, reserves and adjustments can lower it further. One payout covers many orders, so a QuickBooks deposit lines up with no single sale.

02

Refunds land in a different payout than the sale

A refund comes out of your next available payout, not the one the order was paid in, and Shopify doesn't return the original card fee. September's sale and its October refund sit in two deposits and two months.

03

One summary entry, or thousands of receipts

Sync apps tend to post either one summary entry per day or payout, which hides the orders behind it, or one sales receipt per order, which fills the ledger and still has to be grouped before it matches the bank.

04

Tax and gift cards aren't sales

Sales tax you collect is owed to the state, and Shopify doesn't file or remit it unless you use Shopify Tax with automated filing. A gift card sold is money you owe until a customer spends it. Both have to come out of revenue before the books agree.

05

The same product has two costs

Shopify's profit reports leave out any item that sold without a cost on it, and cost per item stays whatever someone last typed. In QuickBooks Online, inventory features come with the Plus and Advanced plans. Margin depends on which cost someone trusted.

What you can finally answer

Eight store-to-books questions you can stop working out by hand

Owners, bookkeepers and accountants ask these every month. Each one shows where the afternoon goes today and what Querri does with Shopify and QuickBooks side by side.

How do I reconcile Shopify payouts to QuickBooks deposits?

Why it's hard

The payout list is in Shopify, the deposits are in QuickBooks, and the amounts are net of fees and refunds, so matching them means two exports and a lookup by date and amount.

With Querri

Querri reads Shopify Payments payouts and every balance transaction behind them, matches each payout to a QuickBooks deposit and lists the ones with no match or a different amount. Save it as a project, put a schedule on it, and it reruns on fresh data. More in reports and automation.

What's our Shopify profit by product once real cost is in?

Why it's hard

Shopify knows price, discount and refund per line. The cost you actually paid sits on supplier bills and items in QuickBooks, and the two drift apart every time a supplier raises a price.

With Querri

Tell Querri once which cost to use in Facts & rules, and it joins Shopify order lines to QuickBooks costs by SKU. Track gross margin by product as a KPI so chat, dashboards and reports show the same number.

Does the sales tax we collected match what's in the books?

Why it's hard

Shopify keeps tax on every order. QuickBooks holds the liability and the payments to each agency. Comparing them by state and month means a report from each and a pivot table.

With Querri

Querri totals tax collected on Shopify orders by state and month, sets it beside the tax accounts in the QuickBooks General Ledger, and shows where they differ. A schedule can send it as a formatted Excel workbook before filing.

How much do we owe on gift cards that haven't been spent?

Why it's hard

Shopify knows each card's remaining balance. QuickBooks has a liability account that someone adjusts by hand, and nobody is sure the two still agree.

With Querri

Querri reads gift card balances from Shopify and the liability from QuickBooks and puts them side by side. It tells you when the numbers can't be tied out, instead of guessing why.

Which channel makes money once ad spend comes out?

Why it's hard

Store sales are in Shopify, Amazon sales and fees in Seller Central, ad spend in each ad platform, and cost of goods in QuickBooks. Nobody has all four in one sheet.

With Querri

Connect Amazon, Meta Ads and Google Ads too. Querri puts spend as the platforms report it beside revenue and margin, so MER, blended CAC and spend against contribution come from one place.

Are we charging enough for shipping?

Why it's hard

What customers paid for shipping is on the Shopify order. What the carrier charged is on a bill in QuickBooks, or in your shipping app, a month later.

With Querri

Querri sets Shopify shipping lines beside carrier costs from QuickBooks or ShipStation, by month and destination. Carrier names spelled three ways are handled by data cleansing.

Can I ask Claude or ChatGPT about my Shopify sales and get the bookkeeper's number?

Why it's hard

An assistant pointed at the store sees gross sales. It doesn't know about fees, tax, gift cards or which cost your accountant uses, so its revenue is a different number every time.

With Querri

Connect Claude or ChatGPT to Querri once. It answers from your Library with your definitions of net sales and margin, and each person gets only the rows their access allows.

Shopify + QuickBooks plus the rest

Add Amazon, your ad spend and your shipping costs

Most brands on QuickBooks sell in more than one place. Amazon settlements, ad spend and carrier bills answer the rest of the margin question. Once connected, they land in the same Library as the store and the books, so one question can reach all of them.

Shopify + QuickBooks pair well with

Answers you can stand behind

"What did we sell in September?" Store and books give different totals. Querri tells you which one you're reading.

The store counts orders placed in September. The books count income posted in September, and depending on how your sync app posts, a late-month order can land in October. Both are fair, and they rarely agree. Querri answers with one, names it, and shows the other beside it. See how answers work.

Wake up to what changed

Querri catches the discount that's eating margin

Every night Querri checks discounts, refunds and fees against their own history, using arithmetic rather than a guess. By morning, anything out of line is listed in your Inbox, and nothing changes without your OK.

Custom Shopify + QuickBooks dashboards

Sales, payouts and margin on one screen

Ask for a dashboard with this month's net sales, payouts still unmatched and margin by product, or start from a screenshot of the one you already keep. The store and the books share one set of definitions there, and a client or location can be limited to its own rows.

  • Store sales next to what reached the books
  • Changed by asking, undone in one click
  • Each person sees only their rows
One sentence in the dashboard chat turns Monthly Sales Review dark, and an undo bar is there if you'd rather not.

Reports you can stop rebuilding

Six Shopify + QuickBooks reports, built once

What comes over

Your store's orders and payouts, and your books, in one Library

Querri copies 24 Shopify tables and 31 QuickBooks Online entities, and each stays current on its own schedule. Querri gets only the access you approve on each connection screen.

A few of the 24 Shopify tables and 31 QuickBooks entities

  • Orders (Shopify)
  • Order line items (Shopify)
  • Refunds (Shopify)
  • Transactions (Shopify)
  • Payouts (Shopify)
  • Balance transactions (Shopify)
  • Products and variants (Shopify)
  • Inventory items (Shopify)
  • Discounts (Shopify)
  • Gift cards (Shopify)
  • Deposits (QuickBooks)
  • Sales Receipts (QuickBooks)
  • Refund Receipts (QuickBooks)
  • Journal Entries (QuickBooks)
  • Accounts (QuickBooks)
  • Items (QuickBooks)
  • Bills (QuickBooks)
  • Tax Rates (QuickBooks)
  • Plus the QuickBooks General Ledger report, loaded in full on every sync

Changes come over on a schedule

Shopify orders sync incrementally by last update, and an edited order re-sends its lines and refunds. QuickBooks entities sync incrementally too. Payouts, balance transactions and the General Ledger reload in full each sync.

Every order, not the last 60 days

Querri reads your store's whole order history through Shopify's bulk API, so a large store loads without hitting rate limits. The General Ledger uses your chosen window, three years by default, on an accrual or cash basis.

Reads only, in both

Querri asks Shopify for read access only and never posts to QuickBooks. No order, product, deposit or journal entry is created, edited or removed.

Approved on each vendor's screen

You approve Querri on Shopify's own screen and on Intuit's sign-in page. Neither password ever reaches Querri, and the Connector Agent sees only whether each connection is working.

How to connect Shopify and QuickBooks

Both connected in one conversation

  1. 1

    Ask the Connector Agent

    Open Connect and say "connect our Shopify store and QuickBooks," or choose each from the catalog.

  2. 2

    Approve Querri in Shopify

    Enter your store name, such as acme or acme.myshopify.com, and approve read access on Shopify's own screen.

  3. 3

    Sign in with Intuit

    Pick the QuickBooks Online company, accrual or cash basis, and how much ledger history to load.

  4. 4

    Approve the load and a schedule

    Nothing loads until you approve it. Choose how often each one syncs, as often as hourly.

  5. 5

    Ask across both

    Ask which payouts aren't in the books. Querri shows how it matched them.

Querri's Connect page with the Connector Agent asking for approval before it starts a connection, next to connector cards for Google Drive, NetSuite, Salesforce, Square, ShipStation and Snowflake
The Connector Agent asks before it creates a connection or loads a single row.

Shopify + QuickBooks FAQ

Questions about Shopify, QuickBooks and Querri

How do I connect Shopify and QuickBooks to Querri?

Open Connect and ask the Connector Agent to connect your Shopify store and QuickBooks, or pick each from the catalog. Enter the store name and approve read access on Shopify's screen, then sign in with Intuit and choose the company and basis. Approve the load and a schedule, and both arrive in your Library.

What Shopify and QuickBooks data does Querri sync?

From Shopify, 24 tables: orders, line items, refunds, transactions, fulfillments, returns, products, variants, customers, inventory, discounts, gift cards, and Shopify Payments payouts with their balance transactions. From QuickBooks Online, 31 entities including deposits, sales receipts, refund receipts, journal entries, accounts, items and bills, plus the General Ledger report.

How often do Shopify and QuickBooks sync?

Incremental syncs can run hourly, daily or weekly and pick up orders and entities changed since the last run. Full refreshes run daily, weekly or monthly; payouts, balance transactions and the General Ledger reload in full each time. You can start a sync by hand whenever you need fresh numbers.

Does Querri change anything in Shopify or QuickBooks?

No. Querri only reads from both. It asks Shopify for read access only and never posts a deposit, receipt or journal entry to QuickBooks. Every question is answered from Querri's synced copy, so orders in your store and reconciled periods in your books are left alone.

Do we still need our Shopify-to-QuickBooks sync app?

Yes, if you use one. It posts sales and payouts into QuickBooks so the books get kept. Querri sits beside it and reads both systems, then shows where they disagree, such as a payout with no deposit or a margin built on a stale cost. It changes neither one.

How do I reconcile Shopify payouts in QuickBooks?

Connect both and ask which payouts don't match a deposit. Querri reads each Shopify Payments payout and the charges, refunds, fees and adjustments behind it, matches payouts to QuickBooks deposits by amount and date, and lists the misses. Your bookkeeper still records the fix in QuickBooks.

How far back do Shopify orders go in Querri?

To the start of your store. Querri has Shopify's permission to read all orders, not only the last 60 days, and loads them through Shopify's bulk API. QuickBooks entities come with their history, and the General Ledger uses the window you choose, three years by default.

Can I connect more than one Shopify store?

Yes. Connect each store separately; every store gets its own tables, labeled with the store's name. Querri can join them with each other and with one QuickBooks company, so total sales across stores or regions appear next to the books in one answer.

How do I get Shopify profit by product with QuickBooks costs?

Connect both and tell Querri once which cost to trust, for example the latest supplier bill in QuickBooks rather than Shopify's cost per item. Querri joins order lines to that cost by SKU, subtracts discounts and refunds, and can track margin by product as a KPI.

How do I get a sales tax report from Shopify and QuickBooks?

Ask for tax collected by state and month. Querri totals the tax on Shopify orders by shipping state and sets it beside the tax accounts in the QuickBooks General Ledger. A schedule can send it as a formatted Excel workbook each month before you file.

How do I combine Shopify, QuickBooks and Amazon data?

Connect Amazon too. Querri brings in Amazon orders, fees, settlements, refunds and returns beside your Shopify orders and QuickBooks books, so you can compare margin by channel after fees and check each Amazon settlement against its deposit the way you do Shopify payouts.

How do I combine Shopify, QuickBooks and Meta Ads data?

Connect Meta Ads, and Google Ads if you use it. Querri puts daily spend as each platform reports it next to Shopify revenue and QuickBooks cost of goods, so MER, blended CAC and spend against contribution margin come from one place. Querri doesn't do ad attribution.

Can I build a custom Shopify + QuickBooks dashboard?

Yes. Describe it in plain words, such as net sales, unmatched payouts and margin by product, or start from a screenshot of the one you keep today. You change it by asking, and each person or client can be limited to their own rows.

Can I export Shopify + QuickBooks reports to Excel automatically?

Yes. Schedule the project behind the report, daily, weekly or monthly. On each run Querri replays the same steps on fresh data and delivers a formatted Excel workbook or an email, and it can produce one version per store, location or client.

Can I ask ChatGPT or Claude about my Shopify and QuickBooks data?

Yes. Connect Querri to Claude or ChatGPT once, and the assistant answers from your Library with your definitions of net sales and margin. Row-level access in Querri still applies, so the answer in Claude matches the dashboard and the person asking sees only their rows.

Can a bookkeeper or fractional CFO manage several Shopify clients?

Yes. Give each client its own workspace with its own Shopify and QuickBooks connections, dashboards and nightly checks, and set row access so each client sees only its data. A scheduled report can send every client their own month-end pack.

What doesn't the Shopify + QuickBooks sync include?

From Shopify: disputes as their own table, refund line items (refund totals do sync), metafields and Shopify's built-in reports. Payouts exist only if you use Shopify Payments. From QuickBooks: reports other than the General Ledger, and QuickBooks Desktop. Incremental syncs don't see deletions until a full refresh runs.

Is my Shopify and QuickBooks data secure in Querri?

Yes. Querri is SOC 2 Type II, HIPAA and ISO 27001:2022 certified, and your data is never used to train a model. You approve access on Shopify's screen and Intuit's sign-in page, so Querri never sees a password, and it only reads from both.

Find out what the store sold and what reached the books.

Connect Shopify and QuickBooks in one conversation. Querri reads both and writes to neither, so every order and every entry stays as you left it.