W1 and W2 amount in "Prepare GST' different from amount in "PAYG Withholding Summary Report"

Thanks for posting in the Community, COPAA!

Let me help you check why your W1 and E1 amount in the Prepare GST is different in the PAYG Withholding Summary Report. One reason is there could be an amendment made on the previously lodged BAS/GST period. Not only the amendment is tracked, but it will also affect your current GST lodgement period.

Here's how to check if there's a PAYG amendment:

1. Click on the Reports tab in QuickBooks Online.
2. On the search box type PAYG and select PAYG Withholding Amendment Report.
3. Check the Accounting method if Cash or Accrual.
4. Click on Run report.

If there's an amendment you'll have to contact our Customer Support team to request the previous GST period to be unlodged to account the changes made after the GST period was lodged.

Another area to check is if the payroll journals have been coded with the correct GST code. And also check the wage expense account if the amount is correct. And lastly, we recommend running a report called Transaction Detail by Tax Code and cross match to the amount in the prepare BAS.

Feel free to reply to this thread if you need more help. I'll make sure to get back to you right away. Have a nice day!