Yes. You can amend your return from filing separately to filing married, jointly. Amended returns can take more than 6 months to process. 

and just in case anyone else reads this thread...yes, in this case the filing status can be amended....BUT

if it had been the other way around (married-joint --> to any other filing status), then NO, you could not do that (unless the amendment occured before the filing deadline)

Thank you for the answer, do I have the same 3 years to do this? Also, if my wife got a refund and I had to pay when we MFS, will this all be automatically recalculated with a new refund amount taking both of our returns into account?

@chubby_2003 - 

any changes to the 2018 tax year had to be made by April 15, 2022, so that is over with

changes to 2019 tax year have to be made by July 15, 2023

changes to 2020 tax year have to me made by May 15, 2024

changes to 2021 tax year have to me made by April 15, 2025

and in each year, if you filed for an extention before the filing deadline, you have until Oct 15 in the years listed.

<<lso, if my wife got a refund and I had to pay when we MFS, will this all be automatically recalculated with a new refund amount taking both of our returns into account?>>

yes, it is effectively a 'do over'.   

thank you!

I am now in the process of amending prior year return from MFS to MFJ. Where do I input the refund (my wife) and payment (me) that was previously done? I see that line 18 on 1040x looks like where it goes. Do I add both mine/hers or enter them separately? The state form is a little more complicated, looks like NJ-1040x line 69 is the overpayment. Again, here do I add hers/mine previous refunds? I put numbers in the worksheet, but the calculation didn't change at the top of turbotax.

It would be better to enter the tax due from your wife's return on line 16 of form 1040-X (line 64 of Form NJ 1040-X) , which is for the payment due on her return.  You would then enter your refund from the original return on line 18 of form 1040-X. Your refund from the amended return would show on line 22 of form 1040-X. If you don't see an amount there, then you need to examine each line entry on form 1040-X to make sure everything is entered correctly. It is possible that your tax is the same after the amendment and that may explain why you don't have a refund from the amended return.

@chubby_2003