I exceeded the limits for Roth IRA contributions (married filing separately) for 2016 and 2017. Should I re-file jointly (if even possible) or pay the 6% penalty?

[falicornia]

I just discovered the income limitation for Roth IRA contributions when filing married but separately (AGI $10000). I would like the money to remain in the Roth account rather than getting it out and paying the penalty.  

[PhyllisG · Accepted solution]

It is possible for you to amend your returns.  You have 3 years from due date of the return or 2 years from the date the tax is paid to file a Form 1040X. This means:

The 2016 return due date was April 15, 2017; therefore, you have until April 15, 2020 to file the amendment and claim the married filing jointly status.  

The 2017 return due date was April 18, 2018; therefore, you have until April 18, 2021 to file an amendment and claim the married filing jointly status.

Your spouse must approve the amendment, because it will also change her status. Both income, deductions, credits, etc must be combined.

Furthermore, if you amend the federal return you must also amend the state.

TurboTax will walk you through the process of amending the returns.

You will have to decide overall if the change of status will result in a balance due that may be more than the 6% penalty. Or, if your preference to retain the money in your Roth IRA is more important than any penalty that may be assessed.

[fanfare]

you don't want to leave an excess in a Roth IRA. The penalty applies every year
when you do take it out, the earnings come out too, and that part is not tax free it is taxable income.