Can someone tell me if the stimulus checks are counted against your refund

[DoninGA]

Stimulus payments are not taxable income and are not entered on a tax return.

[Critter-3]

What may be confusing you  is the program computes the max stimulus payment you are eligible for based on the 2020 info you entered   and that amount is added to the refund total   BUT  at the end of the interview you are asked how much of the stimulus you got in advance and that amount is then  removed from your refund since you cannot get it twice.   NOT the best method/placement  in the interview and for those who watch the Refund-O-Meter like a hawk they can be upset/confused.  

[VolvoGirl]

You are not paying tax on them and it is not deducting it from your refund or increasing the tax due.  Turbo Tax started out by assuming you didn't get it and  giving you credit for the whole amount so your refund was too high to begin with.  Then when you entered what you already got the starting refund was reduced or the tax due increased to your real actual refund.  Otherwise you would be getting the Stimulus amount again on your tax return.

Look at your return.  The Stimulus payments do not show up anywhere as taxable income so you are not being taxed on it.  And it's not being subtracted anywhere.

Check 1040 line 30.  You should only have an amount there if you didn't get the full first 2 Stimulus payments of you qualify for more.  Line 30 either reduces a tax due or increases your refund.