Stripe Payout Doesn't Match Undeposited Funds in QuickBooks Online? How to Reconcile It

Published October 19, 2026 · LedgerMedic

A Stripe payout reaches your bank as one amount, but QuickBooks Online holds the individual payments in Undeposited Funds at their full amounts. The difference is Stripe's fees and any refunds or disputes taken out of that payout. To reconcile it, open the payout in Stripe, build one bank deposit in QuickBooks from exactly the payments it covers, add the fees as a negative line, and make the total equal the bank line to the cent.

The manual fix, step by step

1. Open the payout in Stripe. In the Stripe Dashboard, open the payout from your payouts list. It lists the transactions it contains. Write down the gross total, the fees, any refunds or disputes, and the net payout. The net should equal the line in your bank feed.
2. Find the matching payments in QuickBooks. Open + New then Bank Deposit, choose the bank account, and look at the list of payments under Undeposited Funds. Tick the ones that appear in the Stripe payout. Match them by customer and amount, since several customers may have paid the same amount.
3. Add the fees as a negative line. In the lines below, add a row with your Stripe fees expense account as the account and the fee total as a negative amount. Without it, the deposit is the gross amount and will not tie to the bank.
4. Handle refunds. If you recorded a refund in QuickBooks, such as a refund receipt paid from Undeposited Funds, it may appear in the list as a negative line. Tick it. If you have not recorded it yet, record it first, then come back. Do not hide it inside the fee line.
5. Check the total. The deposit total should now equal the Stripe net payout and the bank line. If it is off, the difference points to the cause: a payment missing from QuickBooks, a payment entered at the wrong amount, or a payment dated into a different payout.
6. Save, then match the bank feed line to it. In Banking, choose Match on the bank line and pick the deposit you just made. Do not choose Add. Adding creates a second deposit and leaves the payments still sitting in Undeposited Funds. See duplicate deposits.

When the numbers still do not tie

• The payment was entered net of fees. If someone typed the net amount as the customer payment, the invoice is underpaid by the fee and the deposit has no fee line to add. Correct the payment to the full amount first, then build the deposit.
• A payout covers several days. Charges from different days can land in one payout, so a deposit built from a single day's payments will be short. Use the Stripe payout's own list, not the date.
• A payment was never recorded. The payout includes a charge that has no payment in QuickBooks. Record it against the right invoice, then build the deposit.
• An old batch is still sitting there. If the account holds payments from months of payouts, work backwards one payout at a time, oldest first. Clearing an old backlog covers the order.

If an app syncs Stripe into QuickBooks

Check how that app records payouts before you fix anything by hand. Some tools create their own deposits, and building a second one yourself would count the money twice. Compare against your bank statement and the Stripe payout, not against what any one tool reports.

Doing it faster

Finding which payments are stuck is the tedious part. The free checker ages a pasted register in your browser with no signup. For the general version of this problem, see Undeposited Funds not matching a bank deposit.

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