Hello in QB advance payroll, in pension with manual setting , not Sync. One of the EEs has asked for 6% (i.e. 5% net for EE) and 5% ER. QB gives different amount. Why?

Thanks for your time posting in the Community, @f-nassiri34-yaho. I'll share an insight on your query to help you fix this issue with pension calculation in QuickBooks Online Payroll. 

The pension calculation depends on your salary on that specific pay run. There are a few things to consider in QBO to confirm if it calculates accurately.

First, we'll need to check how your contributions are set up in your employee's settings. Let me guide you on how: 

1. Go to Employees from the left panel. 
2. Select the Employees tab. 
3. Choose the affected employee. 
4. Go to Auto enrollment section. 
5. Check the percentage under Employee’s contribution and Employer contribution.

Then, you can now proceed reviewing the taxation method that was selected. Here’s how: 

1. Click the Gear icon at the top. 
2. Select Accounts and Settings. 
3. Choose Payroll. 
4. Go to Pension scheme section. 
5. Check the taxation method. 

• Net pay arrangement – pension contribution is deducted before taxes and NICs.
• Relief at source – including tax relief – pension contribution is deducted after deducting tax and NICs,     that is the pension contribution is from the employee’s net pay.
• Relief at source – excluding tax relief – pension contribution is deducted after deducting tax and NICs that is the pension contribution is from the employee’s net pay. However, the employee pays the entire 1% employee contribution.

Please see these articles for more details about workplace pensions:

• Workplace pensions in QuickBooks Online Standard Payroll.
• Manually setup a workplace pension scheme in QuickBooks Online Advanced Payroll.

Keep me posted if you still have questions or concerns about tax calculations in QBO Payroll. I'll be around for you. Have a great day!