To amend from MFJ to MFS, you must file both returns before the April 15 deadline. After that date, changing MFJ to MFS is disallowed by law.
The person who is listed first (top line) of the MFJ return files an amended return as MFS, removing the spouse's income and deductions. The spouse files an original MFS return in their own name, not an amended MFS return. It doesn't matter the order, but you won't be able to e-file the new MFS return. Both must be mailed (separate envelopes) by April 15. Don't forget to also send the appropriate state returns.
Be aware that, if filing with Turbotax online, the new MFS return will require a separate account with a different user name and password. (It can use the same email address for notifications.). This account will also require a separate filing fee unless you qualify for a free return.
Also, be aware that if one spouse itemizes deductions on their MFS return, the other spouse must also itemize, even if they don't have any deductions, and can't use the standard deduction. This removes some of the advantage that people think they get if they don't prepare the MFS returns correctly.
