Duplicate payroll journals in QBO for a single pay run. STP, pay run and payment all occurred once. Is it safe to delete the duplicate journal?

Yes, it is completely safe to delete the duplicate journal entry. This occasionally happens due to a temporary synchronization delay between accounting and payroll systems, which can cause the data to post twice.

Because your Single Touch Payroll (STP) reporting, employee payslips, and bank payments were only processed once, your official records are correct. Deleting the extra entry will simply clean up your accounting reports without affecting your payroll history or tax compliance.

To start, here's how:
 

1. Open one of the duplicate journal entries, click More at the bottom of the screen, and select Delete.
2. Check your payroll dashboard. If it shows a Journal not found error, it means you deleted the copy linked to the pay run. You'll want to click Export/Re-Post Journals inside the pay run to safely regenerate a single, clean copy.
3. Go back to your Payroll Clearing, PAYG Liability, and Superannuation Payable accounts. The doubled balances will disappear, allowing you to reconcile your accounts and finish your year-end finalization smoothly.

For more details on deleting a journal entry, see this article: Reverse or delete a journal entry.
 

You can also consult an accountant, as they can provide alternative ways to handle this situation and keep your books accurate.

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