QuickBooks Online Payment Deposited Twice? Bank Balance Too High After Adding a Deposit

Published October 8, 2026 · LedgerMedic

If your QuickBooks Online bank balance is higher than the real bank's after you added a deposit from the bank feed, the likely cause is that the customer payment was already recorded straight into the bank account, and the feed deposit was added as a second, income-coded transaction. The money is counted twice, in the bank balance and in income. The fix is to delete the income deposit, keep the payment, and match the bank line to it. Every step is below, tedious parts included.

Fix it by hand, step by step

1. Find the payment that went straight to the bank. Open the bank account's register (Accounting > Chart of accounts > View register). Look for a row of type Payment (or Sales Receipt) for the amount in question. A payment that went through Undeposited Funds never shows in the bank register until it is deposited, so a Payment row sitting here means someone chose the bank account in Deposit to.
2. Find the deposit that was added from the bank feed. In the same register, look for a row of type Deposit with the same amount (or the combined amount of several payments), dated within a few days. Open it. If its lines are coded to an income account (Sales, Services, Uncategorized Income) with the customer in Received from, rather than pulling in the payment, that is the second copy of the money.
3. Prove it against the bank. Check the bank statement or the live bank site. If one real deposit of that amount reached the bank, only one of the two QuickBooks rows is real. If two reached the bank, the customer genuinely paid twice and nothing here is wrong.
4. Decide which copy to keep. Keep the payment. It is the one attached to the customer's invoice, so it is what keeps Accounts Receivable and the customer's balance correct. The income-coded deposit is the one to remove.
5. Check the period first. If the deposit is in a month you have already reconciled or closed, check Accounting > Reconcile > History and your closing date before touching it. Removing a reconciled row will break that reconciliation, so tell whoever owns the books and plan to redo that month's reconciliation.
6. Delete the extra deposit. Open the income-coded deposit, note the date, amount and the bank feed line it came from, then use More > Delete. Do this on the deposit, not on the payment.
7. Match the bank feed line to the payment. Go to Banking. The bank line you just orphaned usually returns to For review (if you do not see it, check the Reviewed and Excluded tabs). Click it, choose Match, and select the existing payment. If the original deposit combined several payments, QuickBooks lets you select more than one in the match window; the selected payments must add up to the bank line.
8. Re-check the numbers. The bank register balance should have dropped by the deposit amount and now agree with the bank. Run Profit and Loss for the period: income should be lower by the same amount. Then re-run the reconciliation for the month if it was affected.

Before you delete anything, write down the date, amount and customer on each row. Deleting a transaction in QuickBooks Online is not something you can undo from inside the product.

Why the money is counted twice

A customer payment can be recorded two ways: into Undeposited Funds (and later grouped into a bank deposit), or straight into the bank account with Deposit to set to the bank. The trouble starts when the payment goes straight to the bank and the bank feed later shows the same money as a new deposit. If that feed line is clicked Add instead of Match, QuickBooks creates a second transaction coded to income. Now the bank balance and your income both include the same money twice, once through the payment and once through the deposit.

The version where the payment was left in Undeposited Funds, and a deposit was added from the feed instead of matching, is a different mess: that one leaves the payment stuck. See Undeposited Funds not matching the bank deposit. If instead you can see two deposits that each pull in the same payments, see duplicate deposit in QuickBooks Online.

When doing this by hand is not enough

One occurrence is a ten-minute job. The painful cases are a file with dozens of them across a year, a deposit that combines several payments (you have to find the exact combination), a deposit with cash back or a fee line mixed in (so the amounts no longer match cleanly), or the same Add-instead-of-Match habit repeating every week. Finding them is the slow part: there is no QuickBooks report that lists "income deposits that duplicate a payment".

The faster way