I am an s corp more than 2% shareholder. QB payroll is taxing my health insurance premiums for medicare and social security taxes. WHY?

I'm here to take care of your payroll concern, @kynerlaw.

Yes, you're right. S-Corp owner's health insurance is SS and Medicare tax exempt. You can open this link for more information: Supported pay types and deductions explained.

To get around this issue, let's check the S-Corp pay type. Let me guide you how:

1. Navigate through the Payroll menu, and then choose the Employees tab.
2. Select the employee's name and then click the pencil icon beside Pay.
3. In section 3, choose the pencil icon.
4. Go to the Even more ways to pay employee section. 
5. Choose S-Corp Owner's Insurance.
6. Review the Recurring amount or leave it blank. You'll have the option to enter the S-corp amount when you run payroll.
7. Click Done.
   

After that, you'll have three options on how to proceed. Please refer to this handy article for more details: Set up and record S-Corp health insurance. If you aren't sure what's best to use, you can consult your accountant or tax advisor for further guidance.

If these are transactions from last year, I recommend contacting our support team. This way, they can help you correct your pay type.

Also, we've collated some payroll reports you can run to keep track of your business finances.

Feel at ease to comment below if you need more payroll insights. I've got your back always. Take care!

I did set up the S corp pay type as described prior to requesting assistance and it seems that was what caused the problem I described.I do not know why this happened.

I called the helpline and the support team fixed the issue from their end, and cancelled and regenerated the paycheck. 

thanks.