IRS processed 2021 taxes before 2020, 2021 Estimated payments not seen

[arthurWL]

The IRS indicates it has processed my 2021 electronic return. They have NOT yet processed my 2020 return which was FedEx sent in months late.   However, the IRS stated 2021 refund is for less than my 2021 tax forms indicated the refund should be. It was less by the amount of the 2020 tax refund that I applied as an estimated payment to my 2021 taxes. I believe the IRS subtracted that estimated payment because  they couldn't see the estimated payment since they haven't processed my 2020 taxes.  Hopefully some day the IRS will process my 2020 taxes. But what will happen to that intended 2021 estimated tax payment? Will the IRS still apply it to the 2021 taxes, and if so, how do I get the money back?  Or will the IRS see that the 2020 taxes have already been processed, and send me a check for this estimated 2021 tax payment? Or will they apply it to the 2022 taxes as an estimated payment?  OR, who knows. Any advice would be most welcome. 

[rjs · Accepted solution]

I don't think you should do anything but wait and see what happens after they process your 2020 tax return. You will probably have to wait for months - possibly until the end of this year.

What I think will happen is that they will apply the 2020 refund to 2021 estimated tax. Then sometime later, perhaps several more months later, they will notice that you overpaid for 2021 and they will send you a refund of the excess payment. They will not apply the 2020 refund to 2022.

[Mike9241]

It's good that you still have a refund even though the 2020 overpayment wasn't applied.  otherwise, if the adjusted amount would show you owing the IRS would undoubtedly be sending you a bill.  

[arthurWL]

Your right,  I did  luck out... this could have been even uglier. 

[fanfare]

When your 2020 tax return is processed there is nothing to apply any refund amount to since your 2021 tax return is finished. The specified amount to be applied to next year will be refunded to you.

[Critter-3]

What they will absolutely NOT do is apply it to the 2022 estimated payment ... so even if you did not get the refund by the time you file the 2022 return do NOT enter it as such on the 2022 return.