Guide
How to reconcile Stripe and other processor payouts
One deposit, hundreds of charges, fees and refunds. A practical method for reconciling processor payouts.
Recon AIQ Team · August 25, 2026 · 6 min read
Payment processors deposit net payouts that bundle many charges, minus fees and refunds, often days after the sales happened. If your ledger records sales individually, the bank deposit will never match a single entry.
Use a clearing account
Record sales into a processor clearing account rather than directly to the bank. When the payout lands, transfer it from clearing to the bank. The clearing account should return to zero (or to the amount of pending payouts) at period end.
Match the payout, not the deposit
- Pull the processor's payout report — it lists every charge, refund and fee in each payout.
- Match each payout ID to the bank deposit.
- Match the charges in that payout to invoices or sales receipts.
- Record fees and refunds from the report as separate lines.
Watch for timing
Payouts settle on a schedule, so sales at the end of the month often land in next month's bank statement. Those belong on your list of deposits in transit, not in the difference column.
Recon AIQ automates this by treating a payout as a one-to-many match and breaking out fees and refunds automatically — but the clearing-account method works with any tool.