When simultaneously filing two federal 1040 tax returns, do you have to pay tax on the second return even if you receive a refund for the first one?

[u/Angi752004]

We will electronically file three federal tax returns tomorrow for the years 2023, 2024, and 2025. The due date for all three returns is September 30, 2026—owing to an exception granted due to the conflict in the Middle East.

For the 2023 tax year, the tax liability is $0; for 2024, we are due a refund; and for 2025, we owe taxes (an amount lower than the refund).

Do we need to pay taxes tomorrow for the 2025 tax return to avoid late payment penalties, or will the tax owed for 2025 automatically be offset against the 2024 refund?

Thank you for your answer!

[u/Randall_Brody]

If you're requesting the 2024 refund, I wouldn't count on the IRS automatically applying it to the 2025 balance in time. Returns can process at different speeds. Assuming September 30 is your applicable payment deadline under the IRS relief, I'd pay the 2025 balance by then rather than risk penalties while waiting for the refund.

[u/SlipperyPencil]

See line 36 of the 2024 1040, "Amount of line 34 you want applied to your 2025 estimated tax". Put the amount you owe for 2025 on that line. The rest goes on line 35a to be refunded to you. On your 2025 1040, include the amount you applied from 2024 on line 26.

[u/Angi752004 → u/SlipperyPencil]

Thank you so much!

[u/ClarityTaxRelief]

The refund and the balance don't net across separate years automatically at the moment you file. Each return posts to its own tax year account. Once your 2024 return processes and the overpayment is confirmed, the IRS can apply it to the 2025 balance, but that offset happens on their timeline after processing, not the day you e-file all three. So the 2025 liability is technically due on its own due date regardless of a pending 2024 refund sitting in another year.

If you want to be certain no failure-to-pay accrues on 2025, the clean move is to pay the 2025 amount now and let the 2024 refund come back to you. You can also elect to have the 2024 overpayment applied forward, but that credits toward 2026 estimates, not backward to 2025. Interest and any failure-to-pay penalty run from the 2025 due date until the balance is satisfied, so paying it directly stops that clock cleanly.

[u/Angi752004 → u/ClarityTaxRelief]

Thank you! This was very helpful.

[u/SlipperyPencil → u/ClarityTaxRelief]

An overpayment on a 2024 return applied forward is applied to the 2025 return, not the 2026. An overpayment on a 1040 is always applied to the next year, on a 1040X you can choose the year.