Married filing separately

My income is $100k and my spouse is $45k.  When I complete everything as married filing separately with myself taking the mortgage, student loan interest deductions, we pay about $1000 less than married filing jointly.  We do not itemize and I just take the standard deduction with the home mortgage and student loan interest on mine (the house is jointly owned but the student loans are all mine), Is this ok to do?  I mean we still owe but its just less this way.
    It's not quite clear what you did on each of the two separate returns. You said "I just take the standard deduction with the home mortgage and student loan interest on mine." But home mortgage interest is an itemized deduction. You can't deduct it if you take the standard deduction. Also, you cannot take the student loan interest deduction at all if your filing status is marrried filing separately, regardless of whether you itemize deductions or take the standard deduction.

    If you file as married filing separately you cannot itemize deductions on one of the returns and take the standard deduction on the other. You have to either both itemize or both take the standard deduction. If you prepared the two separate returns with itemized deductions on one and the standard deduction on the other, that could be why it looks like you would pay less.

    Review the two separate returns and make sure the filing status is married filing separately on both of them. Also make sure that they either both take the standard deduction or both take itemized deductions. Then see if the combined result of the two married-filing-separately returns is still less than the married-filing-jointly return.

    In TurboTax Online, which is what you appear to be using, you should be doing this with three separate user IDs - one ID for the joint return and one ID for each of the separate returns. If you change the filing status on one user ID from joint to separate it is likely to cause errors, especially if you then change it back to joint. If you did that, I would recommend clearing the return and starting over.
      If you file separately, if one itemizes, the other has to itemize, if one takes the standard deduction, the other one has to take the standard deduction.    It would be very unusual under these circumstances that you have described that you would be better off filing separately.   You can check it both ways using the rules I have described that are required.  Make sure when you compare that you only claim yourself and not her and vice versa.  You cannot mix itemizing and non-itemizing on separate returns when you are married.
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