Thank you for reaching out about the duplicate transactions you see in QuickBooks Online when you run payroll and manually pay employees by e-transfer, Leanne. I understand how this can be confusing. Let me help you streamline this process and ensure your records remain precise and accurate.
Based on your situation, QuickBooks records the payroll paycheck once when you run payroll. Then, when you manually pay your employees via e-transfer from your bank account, that payment appears as a separate transaction in your bank feed. This causes the same payroll payment to show up twice in your records once as the payroll expense and once as the bank transaction.
To resolve this and prevent duplication, when the e-transfer transaction appears in your bank feeds, you should either match the bank feed transaction to the payroll expense if QuickBooks suggests a match, linking the payment to the payroll already recorded; otherwise, exclude the transaction to avoid recording it twice.
Here's how to exclude a transaction:
- Navigate to the Transactions menu, then select Bank transactions.
- Select the For Review tab.
- Click the checkbox of the specific transaction to exclude.

- Lastly, hit Exclude.
Additionally, you can check out this article for further guidance on efficient payroll management and how to access and generate comprehensive payroll reports: Run payroll reports in QuickBooks.
Don't hesitate to ask for help if you have questions about adding expenses to your employees' paychecks or creating related transactions in QBO, Leanne. The Community is here to assist you with any other concerns.