6:31 pm PDT March 21, 2015
If your bookkeeper told you that if you filed separately that your SS would not be taxed and you would not have to file a return, your bookkeeper may have been seriously mistaken.
If you are married and you live together and you file separately, and you get SS benefits, there is a special rule that requires you to include your SS benefit in gross income when deciding whether you have to file, and if you have to file, then 85% of your SS benefit is taxable regardless of how much other income you have.
Each year you can choose to file as Married Filing Separately. However, that may not provide the benefit that you expect, and you will almost always end up paying more in tax than if you file jointly.
The Married Filing Separately filing status is very different than the Single filing status. There are a number of severe restrictions on deductions and credits, and on the amount of IRA contributions that you can deduct, especially if you live together with your spouse.
You can not take the EIC,
You can not take the credit for Child and Dependent Care,
in most cases,
You can not take the Education credits/deductions, and there are many other restrictions.
If either of you receive Social Security benefits and you live with your spouse, more of the SS benefit will be taxable, and the person receiving it will have to include the SS benefit in their gross income when determining whether they have to file. If one of you itemizes deductions, the other must also itemize even if they have nothing to itemize.
Before you decide, you should carefully read the restrictions that go with MFS in IRS Pub. 501, at this link:
You should carefully read the limits on IRA deductions in IRS Pub. 590 at this link:
In addition, if you live in a Community Property state, there are special rules you must follow for reporting income and expense. For further information on that, see IRS Pub. 555, at this link:
As far as filing amended returns, in general, after the due date of a return you can not file an amendment to change from Married Filing Jointly to Married Filing Separately, so you could not file an amended return for any year before 2014.
See the Instructions for Form 1040-X at this link