This is almost always a categorization issue, not a real duplicate. When a deposit is categorized to the same bank account it lands in, QuickBooks adds an offsetting payment that cancels it out, so it shows as both a deposit and a payment. The fix is to change the category to the correct income account, or whatever account the money actually belongs to. Then, the phantom payment clears on its own. Please do not delete the entry to fix this, since that removes the real deposit and can throw off your reconciliation.
Fix a deposit that shows as both a deposit and a payment
- Go to All apps, then Accounting, then Chart of accounts, find the bank account, and select View register.
- Select the affected transaction to expand it, then select Edit.
- In the Category (or Account) field, choose the correct income account, not the bank account itself, then Save.
- The offsetting payment clears automatically, leaving just the deposit.
If the transaction is still in the For review tab, open it, set the correct category (not the bank account), then add it. See Categorize online bank transactions in QuickBooks Online.
Recording a deposit manually? Pick the right accounts
- Select + Create, then Bank Deposit.
- At the top, in the Account field, choose the bank the money goes into.
- Under Add funds to this deposit, set the Account column to the correct income or source account, not the same bank account.
- Confirm the total matches your real deposit, then Save.
Full steps: Record and make bank deposits in QuickBooks Online.
If instead you have true duplicates (many entries doubled or tripled)
- Go to Transactions, then Bank transactions, and open the For review tab.
- Check the genuine duplicates and select Exclude (do not delete posted ones).
- Confirm the same bank account isn't connected twice, which can download everything a second time.
- If balances still look wrong after that, contact support so they can review your account: select Help, then Search, then Contact Us.
A note on direct deposit contractor payments
If the paired entry is a 1099 contractor or payroll direct deposit, that pairing is part of how direct deposit records the payment, and you can't delete it. If the payment hasn't processed yet, you can void it instead. Reach out if you need help confirming the status before voiding.
If you are on QuickBooks Desktop
The same principle applies: don't categorize the deposit to the bank account. To set aside a transaction the bank sent in error, open the Bank Feeds Center, select the account's transaction list, check the item, then use Batch Actions, then Ignore.
Official sources drawn from: