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It depends. It's usually best to do test returns, including your state return to see if there is an overall savings. However, if I understand you question, you thoughts are that if your return income was lower and your tax return is used to consider the possible loan payment reduction, unfortunately we cannot answer that for you. My advice would be to contact an expert in the student loan process to help you with that decision, or a financial advisor specializing in this area.
For the tax return here are some consequences of filing separately, without consideration for your state return implications.
Married filing separately (MFS) does carry penalties that may or may not affect you. There is no special direct penalty. However, the MFS filing status does not allow the taxpayer certain deductions and credits that might be available to other filing statuses. It is by far the WORST filing status in the tax laws under most circumstances.
It is uncommon that MFS is a better choice than MFJ. Many of the people who believe they are better off MFS think that because they are not preparing their returns properly. Three well-known items that are not available to MFS filers are the Earned Income Credit, the Child and Dependent Care Credit and any of the education deduction/credits (American Opportunity, Lifetime Learning, Tuition and Fees Deduction).
Additionally, if one spouse itemizes deductions, the other spouse must also itemize deductions and is precluded from using the standard deduction (this may not pertain to you if your spouse is not required to file a return).
It's best to try it both ways to see find the most advantageous way to file. You can complete your return, check the end results (refund or amount owed), then add your spouse to your return in 'My Info' to check those results. You can always go back to take your spouse off.
For TurboTax Desktop there is a 'What if Worksheet' that allows you to see comparisons.
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