--- title: "Reconcile Stripe & Square Deposits to Sales | MCC Solutions" description: "Use a clearing account to match payouts, fees and refunds. Worked weekly example." url: "https://mcc-solutionsnj.com/bookkeeping/guides/reconciling-payment-processor-deposits" --- Bookkeeping guide · Updated October 12, 2026 # Reconciling Stripe and Square Deposits to Sales A deposit from a payment processor is not the same as your sales. Fees, refunds, chargebacks and timing all sit in between. If you book each deposit as income, your revenue is understated and your fees are invisible. By [Matthew Coleman](/about), MCC Solutions **Quick answer.** To reconcile a processor deposit, compare gross sales, processor fees and the net payout: gross sales minus fees, refunds and adjustments equals the amount sent to your bank. Record the gross amount as income and the fees as an expense. Want this handled for you? Monthly bookkeeping, cleanup and year-end close for small businesses. Start with a free health check of your books. [Free health check](/bookkeeping/health-check)[Get a quote](/bookkeeping/#interest) **Related:** [NJ 1099 contractor rule (ABC test)](/bookkeeping/guides/nj-independent-contractor-rule-abc-test-2026) · [Trial balance explained](/bookkeeping/guides/trial-balance-explained) · [Owner contribution or loan](/bookkeeping/guides/owner-equity-and-capital-contributions) **Free tools:** [Mileage deduction calculator](/bookkeeping/mileage-deduction-calculator) · [Current ratio calculator](/bookkeeping/current-ratio-calculator) Sell in more than one place? The [Sales-Channel Profit Tracker](/toolkits/sales-channel-profit-tracker) shows which channel makes money after fees, costs and booth fees. [![Intuit ProAdvisor Gold tier badge](/img/credentials/intuit-proadvisor-gold.png)](https://proadvisor.intuit.com/app/accountant/search?searchId=matthew-coleman77)Gold tier in Intuit's ProAdvisor program. [See my Intuit listing](https://proadvisor.intuit.com/app/accountant/search?searchId=matthew-coleman77) Keeping your own books? Tallyfinch does invoices, bank import and reports on your computer. [See Tallyfinch](/bookkeeping/mcc-books-downloadable-bookkeeping-software) ## The three numbers There are three things to compare: gross sales, processor fees and net payout. Gross sales minus fees, refunds and adjustments equals the amount sent to your bank. Your books should record the gross amount as income and the fees as an expense. Recording only the net deposit hides the fees, understates sales and may affect sales tax reporting and your tax return. ## Use a clearing account Create a processor clearing account. Record gross sales into it as they happen. Record fees and refunds against it. When the payout arrives in the bank, move it out of the clearing account. At the end of each period the clearing balance should be small and explainable, such as sales not yet paid out. This structure turns a confusing situation into a simple reconciliation. ## Matching a payout Download the payout report from the processor. It lists the sales, fees and adjustments that make up each deposit. Compare it with what you recorded. Many platforms integrate directly with accounting software and create the entries for you, but verify them against the report. If an integration is used, check how it records tips, taxes and gift cards, since those can land in unexpected accounts. ## Timing differences Sales made on the last days of the month often pay out in the next month. That is why the clearing account balance should equal sales awaiting deposit. Check the first payout of the new month to confirm. Delayed or held payouts, reserves and failed payouts also create differences. Contact the processor if an expected payout is missing. ## Fees, taxes and tips Fees can be per transaction, monthly or for added services. Categorize them as merchant fees, and run the total each quarter to see the real cost of accepting cards. Sales tax collected should go to a liability account, not income, and tips owed to staff go to a payable. Monthly, compare processor gross sales with the sales in your books. They should agree after allowing for refunds and timing. If they do not, find the gap before you file sales tax or tax returns. ## A small reconciliation example Say a week of card sales totals a round gross figure, fees come to a small percentage, and one refund was issued. The payout in your bank equals gross minus fees minus the refund. In the books, gross sales go to income, fees to merchant fees, the refund to sales returns, and the payout clears the processor account. If the bank deposit does not equal that math, one of the pieces is missing and the payout report will show which. If you use more than one processor or marketplace, give each its own clearing account so problems stay isolated. Reconcile each to its own payout report, then total them against the revenue section of your profit and loss. ## Worked example with numbers Sales for the week are $5,400 gross. The processor deducts fees of $156.60 and refunds of $120, so the deposit should be $5,400 - $156.60 - $120 = $5,123.40. Record sales $5,400, fees $156.60 and refunds $120 through a clearing account, then the $5,123.40 deposit clears it. If the bank shows $5,100, you are $23.40 short: look for a dispute or a fee not in the report. ## Mistakes that cost money Recording deposits as sales. Missing tips and sales tax in the gross. Ignoring timing at month end. ## Check your work The clearing account should be zero or equal to the amount in transit. ## Common questions **Should I record the net deposit as income?** Generally no. Record gross sales and show fees as an expense. **Where do I find fees?** In the processor dashboard under reports, statements or payout details. **What about disputed payments?** They show as adjustments or withdrawals. Record them as chargebacks and track the outcome. This guide is general information, not tax, legal or accounting advice. Rules, fees and due dates change; check with the IRS, the NJ Division of Taxation or a licensed professional for your situation. Let us handle it [### Monthly bookkeeping Categorizing, reconciling and monthly reports, with cleanup, payroll and NJ filings available. Bookkeeping →](/bookkeeping/) [### Square, Stripe and payment processors How sales from Square, Stripe, PayPal and other processors should flow into your accounting software, and why deposits never match sales. Square & Stripe →](/bookkeeping/software/square-and-stripe)[### QuickBooks Online Monthly bookkeeping, cleanup and reconciliation in QuickBooks Online for New Jersey small businesses. Your account stays in your name. QuickBooks →](/bookkeeping/software/quickbooks-online) More guides - [What Is a Trial Balance and How to Use One](/bookkeeping/guides/trial-balance-explained) - [Closing Entries and Retained Earnings Explained](/bookkeeping/guides/closing-entries-and-retained-earnings) - [Cost of Goods Sold Explained for Small Business](/bookkeeping/guides/cost-of-goods-sold-explained) - [Gross Margin vs Markup: Stop Mixing Them Up](/bookkeeping/guides/gross-margin-vs-markup) Free tool - [Bookkeeping health check](/bookkeeping/health-check) [All guides](/bookkeeping/guides) Reach small business owners, freelancers and bookkeepers who read this guide: [advertise here](/advertise#bookkeeping). Do it yourself ### Month-End Close Workbook A real month-end close in one Excel file. It tells you when a rec does not tie, which variances still need an answer, and when the period is ready to lock. [See what's inside ($19)](/toolkits/month-end-close-workbook)14-day full refund Course: [Small Business Bookkeeping Basics](/courses/small-business-bookkeeping-basics) ($49) covers chart of accounts, reconciliations, the monthly close, payroll and 1099 basics for owners. It is training with a certificate of completion, not a credential. [![Cover of Bookkeeping Fundamentals (ebook) by Matthew Colt](/img/toolkits/bookkeeping-fundamentals-ebook/cover.webp)](/toolkits/bookkeeping-fundamentals-ebook) From the bookshelf ### Bookkeeping Fundamentals A college-level bookkeeping course, without the tuition. By Matthew Colt, $9.99 as an ebook (EPUB and PDF). [See the book](/toolkits/bookkeeping-fundamentals-ebook) [Read the first pages free](/toolkits/bookkeeping-fundamentals-ebook#free-starter) Free tool ### Payout reconciliation calculator Check whether a Stripe, Square or PayPal deposit matches its sales, refunds, fees and disputes, and get the entry that books it. It runs in your browser and nothing you enter is saved. [Open the payout reconciliation calculator](/bookkeeping/stripe-square-payout-reconciliation-calculator) Tallyfinch ### Books you keep on your own computer Tallyfinch does invoices, bills, bank import, reconciliation and the main reports, in a file you own. $99 once, then $5 a month for updates; the app keeps working if you stop the plan. It does not do payroll or sales tax filing. The free download records up to 60 entries. [See Tallyfinch](/bookkeeping/mcc-books-downloadable-bookkeeping-software) [Download it free](/tools/pro/trial/mccBooks) [Compare the three apps](/software) ## Rather have us keep the books? 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