If card sales and a bank deposit do not match, reconcile the processor's payout batch before changing your bookkeeping. The deposit can reflect processing fees, refunds, other adjustments, and a different cutoff period from your sales report. A smaller deposit is not, by itself, evidence of missing revenue.
Start with one bank deposit, its matching processor payout, and the transactions included in that payout. This is a narrower job than reconciling an entire accounting period—and usually a better first test than buying another integration or forcing the difference into a miscellaneous expense.
Why a daily sales total can be the wrong starting point
A sales date tells you when a sale was recorded. A settlement or availability date tells you when its funds became available under the processor's rules. A bank posting date tells you when the receiving bank recorded the transfer. Those dates do not have to be identical.
Square notes that payments accepted after a daily transfer cutoff can appear in a following transfer. Its Dashboard lets you inspect a transfer's included payments and export transaction details. See Square's guide to matching transfers to sales. Check the specific location too; the wrong location can make a correct report look incomplete.
Do not solve a date mismatch by moving a genuine sale to an arbitrary day. First document which report uses which clock and which transaction population.
Worked example: $1,000 of charges becomes $873
Assume one hypothetical payout contains $1,000 of captured card charges, a $100 refund deduction, and $27 of actual posted processing fees. For clarity, this example has no sales tax, tips, disputes, reserves, currency conversion, loans, or other adjustments. The $27 is an invented report amount, not a quoted Square or Stripe fee schedule.
| Batch component | Amount | Evidence to match |
|---|---|---|
| Captured charges | +$1,000 | Included transaction IDs |
| Refund deduction | −$100 | Refund record and linked original charge |
| Posted fees | −$27 | Processor fee rows |
| Expected payout | $873 | Processor payout record |
| Bank deposit | $873 | Bank transaction reference |
| Unexplained difference | $0 | $873 − $873 |
The $127 gap from gross charges is explained: $100 of refunds plus $27 of fees. Recording the entire $127 as processing fees would conceal the refund. Recording $873 as an additional sale, after the $1,000 sales records have already been imported, could count the same underlying activity twice.
Use the processor's actual signed adjustments. Do not assume a refunded payment also returns its original processing fee. If taxes, tips, or other amounts are included in your real transactions, separate them according to your accountant's mapping rather than treating every dollar collected as your revenue.
Choose the report that matches your payout method
Stripe's Payout reconciliation report links automatic payouts to settlement batches and offers itemized downloads. Manual-payout users generally need the Balance report instead. Stripe also explains that instant payouts do not identify a specific transaction batch in the same way; the user must reconcile them against transaction history.
That distinction changes the workflow. Do not promise a perfect one-payout-to-one-batch match when the payout method does not provide one. In that case, reconcile activity through the processor balance over a defined period and match transfers out to bank deposits separately.
The balance test catches money still in transit
A period-level reconciliation is a bridge between opening and closing processor balances. Here is a separate hypothetical period using the same amounts: an opening $200 balance, $1,000 of new charges, $100 of refunds, $27 of fees, and $873 transferred out.
Ending processor balance: $200 + $1,000 − $100 − $27 − $873 = $200.
The $200 closing balance is not automatically an error or an expense. It is an amount that must be explained by the processor's ending-balance detail. Depending on the actual records, funds could be pending or otherwise not transferred yet. The equation proves the totals reconcile; it does not prove that every underlying transaction is legitimate or available for withdrawal.
If the processor reports $225 instead, the unexplained difference is $25. Find the missing or misclassified entry. Do not invent a $25 “bank fee” merely because it makes the equation balance.
A repeatable six-step reconciliation
- Save the bank evidence. Record deposit amount, currency, posting date, and reference. Check the intended receiving account.
- Find the processor transfer. Match amount and reference, then confirm location, currency, and status. A matching amount alone is weak evidence when deposits repeat.
- Export the supporting transactions. Keep payout or transfer IDs, charge IDs, refunds, signed adjustments, fees, and relevant dates.
- Build the bridge. Add charges, subtract deductions, and include other signed adjustments exactly once. Compare the result with the transfer amount.
- Trace the bookkeeping records. Determine whether sales already came from an invoice system, POS connector, or manual entry before accepting a bank-feed suggestion.
- Close or document the exception. Save the matched evidence, or assign the unresolved amount to a named reviewer with a next action.
Use a worksheet with these columns: payout ID, bank reference, expected net, bank amount, difference, evidence location, owner, and resolution. Keep customer details out of broadly shared notes; transaction identifiers and a secure evidence reference are usually enough for internal follow-up.
When to stop and escalate
If the processor marks a transfer failed, points to an unfamiliar destination, or lists an adjustment you cannot explain, preserve the records and contact the appropriate provider or accountant. Do not trigger another customer charge or refund to make the report match.
Likewise, if resolving the difference would require editing a closed accounting period, stop the routine reconciliation. Let the person responsible for your books decide whether and how to correct historical entries. The goal is supported records, not a cosmetically perfect zero.
Common questions
Should the processor clearing balance always be zero?
Not necessarily. Pending activity and payout timing can leave a legitimate balance. Every remaining amount should have an explanation and supporting detail.
Can I combine all processors into one worksheet?
Use separate sections by processor, account, location where relevant, and currency before consolidating. Combining everything too early can hide an overstatement in one source behind an understatement in another.
Do I need a paid reconciliation app?
First prove one representative payout manually. That gives you a test case for evaluating any existing connector or future tool. Automating an unexplained mismatch makes it harder to identify which system introduced the difference.
Next, reconcile one deposit and save its evidence. If you are choosing a workflow, read our Square and Stripe service-business comparison. If the problem is instead a prior reconciliation's opening figure, use the QuickBooks beginning-balance checklist.
Prepared September 20, 2026. Provider documentation checked on that date; account permissions and interfaces may differ. Educational workflow, not individualized accounting or tax advice. All example amounts are hypothetical.