There is no special direct penalty. However, the Married Filing Separately filing status does not allow the taxpayer certain deductions and credits that might be available to other filing statuses. MFS 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.
The "Married Filing Separately" filing status carries higher tax
rates than the “Married Filing Jointly” filing status. Also, many deductions and credits that are
available to MFJ filers are not available to MFS filers. Three well-known such
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.
People usually use MFS when they can't agree to file jointly. Occasionally, the
right combination of situations will create a smaller total tax than on a joint
return, such as when one spouse has significant medical expenses, but it's
rare.
About the only advantage to filing separately is that one spouse is not responsible
for what's on the other's return (including the tax).
Regarding that last comment, you can still use the MFJ filing status and include a Form 8379 Injured Spouse Claim with your return. This protects any refund of one spouse in a joint return from being used to satisfy the debts and/or obligations of the other spouse. The Form 8379 is included within TurboTax under Federal Taxes, Other.
I am told that married persons filing tax returns in Ohio may be able to benefit from filing their Federal returns separately to significantly reduce their state tax obligations. Ohio filers should take this into consideration in evaluating the above comments.
I started Turbo Tax filing jointly, entered my W-2 and my federal refund was over $2,700. After entering my wife's W-2, our refund went down to $680. After removing her W-2 and trying to file separately, it stayed at that amount. I removed both W-2 forms, then tried starting over and doing this separately and now after entering my W-2, it stays at $680. Something isn't right because it looks exactly as it did when first getting a refund of over $2,700. @Howard1948
You can’t change your return around like that. You need to set up new accounts to compare Joint to MFS.
That's common for your refund to be reduced when you add more income. It just looks that way because you put them in as separate W2s and saw the tax due change in between them. If it all was on one W2 you would get the same answer. And each job was withholding like it was your only job.
Because you only get one standard deduction and personal exemption (or 2 for Joint), no matter how many W2s you put in. Turbo Tax starts out by giving you the Standard Deduction. You entered more income when you entered the second W2 but you didn't enter more deductions. And each job only withheld taxes like it was your only job for the year. You might want to adjust your withholding. Also as you add more income you might not be getting as many credits as before like the EIC credit. And it was probably giving you the EIC credit until you went over.
See, <a rel="nofollow" target="_blank" href="https://ttlc.intuit.com/questions/2273878-why-did-my-refund-drop-when-i-entered-another-w-2">https://ttlc.intuit.com/questions/2273878-why-did-my-refund-drop-when-i-entered-another-w-2</a>
I would like to add, the reason I do not file jointly is due to how much my student loan repayment would be. It would go off my tax returns and include my husband's salary. Therefore, my payments would double or more. I wouldn't be able to pay them, and I would be paying a lot more in the long run given I qualify for public student loan forgiveness. I wish I could file jointly, but it just doesn't work great for me. Both situations aren't great, but one is better than the other.