QuickBooks Payments
Intuit’s own card-and-ACH processor records inside QBO automatically — but it still deposits net of fees, so the fee has to be split out or the deposit won’t match the bank.
QuickBooks PaymentsQuickBooks® Online
QuickBooks Online integrations setup guide
Connecting an app to QuickBooks is easy. Reconciling it is where the books break.
Connecting an app to QuickBooks takes a few clicks — reconciling it is where books break, since most integrations post net of fees and must be mapped right. This hub routes to a plain-English page for all nine QBO integrations.
Bookkeeping & advisory · not these apps · We set up and reconcile the data flow in your file
QuickBooks · OnlineIntegrationsBy TechBrot2026-10-15
§ 01 · In short
All nine QuickBooks Online integrations, and where each one breaks the books.
§ In short
Connecting an app to QuickBooks Online takes a few clicks. Reconciling it is where the books break. The recurring problem is the same across almost every integration: money comes in net of fees, or entries post against accounts that must be mapped correctly first, or the file simply won’t reconcile. This hub routes to a plain-English page for all eight common QBO integrations, grouped by what they do — payments & POS (QuickBooks Payments, PayPal, Square), ecommerce (Shopify), bills & expenses (Bill.com, Expensify), payroll (Gusto), and CRM (HubSpot) — with the one gotcha that breaks each one. As TechBrot — not Intuit, and not affiliated with any of these apps — we set up the data flow and make it reconcile in your file. Already connected something that won’t balance? Start with QuickBooks cleanup.
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§ 02 · Payments & POS
Taking payments.
Card, online, and in-person payments flowing into QBO — almost always net of processing fees.
PayPal
PayPal mixes sales, fees, transfers, and its own balance in one feed. Treated as a plain bank account it double-counts income; it has to be reconciled as the clearing account it really is.
PayPal + QBOSquare
Square deposits daily takings net of fees and lumps tips, refunds, and sales tax together — the daily payout has to be broken back out into its parts or the sales and tax numbers are wrong.
Square + QBO§ 03 · Ecommerce
Selling online.
Storefront orders, fees, and sales tax landing in the books.
Shopify
Shopify orders, shipping, discounts, sales tax, and payout fees all need mapping to the right accounts — sync it raw and revenue is overstated while the Shopify payout never reconciles to the bank.
Shopify + QBO§ 04 · Bills & expenses
Paying bills and tracking spend.
Accounts payable and employee expenses feeding into QBO.
Bill.com
Bill.com pays vendors through its own clearing account, so payments hit QBO as a transfer, not a bank withdrawal — map it wrong and bills look unpaid or get recorded twice.
Bill.com + QBOExpensify
Expensify pushes expense reports into QBO as bills or card charges — useful, but every expense category has to be mapped to a real account or reimbursements and card spend land in the wrong place.
Expensify + QBO§ 05 · Payroll
Paying your team.
Wages, taxes, and withholdings posting to the books.
Gusto
Gusto is a separate payroll platform that Intuit lists among the apps that connect to QuickBooks Online. However payroll arrives, wages, employer taxes, and net pay need their own accounts — mapped to a catch-all, they land lumped together. We set up and support Gusto payroll alongside QuickBooks.
Gusto + QBO§ 06 · CRM
Sales and customer data.
Keeping the CRM and the books in sync without double-counting.
HubSpot
HubSpot syncs deals, contacts, and invoices with QBO — powerful for sales, but if both systems create invoices you double-count revenue, so it has to be set up with one source of truth.
HubSpot + QBO§ 07 · FAQ
QuickBooks Online integrations questions.
Which apps do you integrate with QuickBooks?
The common ones businesses actually run — the eight on this page: QuickBooks Payments, PayPal, and Square for taking payments; Shopify for ecommerce; Bill.com and Expensify for bills and expenses; Gusto for payroll; and HubSpot for CRM. As TechBrot we set up and reconcile these connections inside your own QBO file — we don’t sell the apps and we aren’t affiliated with them.
Why do integrations break the books?
Two recurring reasons. First, net-of-fees deposits: Stripe, PayPal, Square, Shopify, and even QuickBooks Payments pay out the money you collected minus their processing fee, so the deposit never matches gross sales unless the fee is split out separately. Second, bad account mapping: every app posts entries against accounts in QBO, and if sales, fees, refunds, sales tax, payroll, and payouts aren’t mapped to the right accounts, revenue gets overstated or double-counted and the file won’t reconcile. Connecting the app is one click; making it reconcile is the work.
Are you affiliated with these apps or Intuit?
No. TechBrot is a bookkeeping and advisory firm. We are not Intuit, not Intuit’s official software support, and not affiliated with Stripe, PayPal, Square, Shopify, Bill.com, Expensify, Gusto, or HubSpot. Those names are trademarks of their respective owners, and QuickBooks and Intuit are registered trademarks of Intuit Inc. We just configure these tools to work correctly together in your file.
Can you fix a messy integration that's already connected?
Yes. A connected-but-wrong integration is one of the most common reasons a file stops reconciling — net deposits left as income, duplicated invoices, payouts that never tie out. We untangle the entries, fix the mapping, and rebuild the reconciliation. See QuickBooks cleanup for how that work runs, and the file review will tell us how deep the mess goes.
Do you set it up for me?
Yes — in your own QuickBooks Online file, with your senior bookkeeper. We connect the app, map every account it touches, configure how sales, fees, refunds, and payouts post, and prove it reconciles to the bank. Your data stays in your file; we keep the books CPA-ready and coordinate with your CPA or EA, who files.
Where do I start?
With a free QuickBooks file review. We look at how your apps connect to QBO today — what’s mapped where, what’s posting net of fees, and what isn’t reconciling — and show you exactly where setup or cleanup will help. No pitch, no obligation. Independent firm, not Intuit, and not affiliated with these apps.
Start with your real file
We'll set up the integration — and make it reconcile.
Tell us where the books stand. We’ll tell you which engagement fits, if any.
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