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You lose some child-related credits if you file married filing separately. We do not know the ages of the children involved--if anyone is a college student, you cannot get education credit if you file MFS. You also lose earned income credit and the childcare credit.
We cannot comment or guess at the health related benefit your daughter receives.
JOINT vs. SEPARATE RETURNS
If you are legally married at the end of 2025 your filing choices are married filing jointly or married filing separately when you prepare your 2025 return next year.
Married Filing Jointly is usually better, even if one spouse had little or no income. When you file a joint return, you and your spouse will get the married filing jointly standard deduction of $31,500 (+ $1600 for each spouse 65 or older) for 2025. You are eligible for more credits including education credits, earned income credit, child and dependent care credit, and a larger income limit to receive the child tax credit.
If you choose to file married filing separately, both spouses have to file the same way—either you both itemize or you both use standard deduction. Your tax rate will be higher than on a joint return.
Some of the special rules for filing separately include: you cannot get earned income credit, education credits, adoption credits, or deductions for student loan interest. A higher percent of your Social Security benefits may be taxable. In many cases you will not be able to take the child and dependent care credit. The amount you can contribute to a retirement account will be affected. If you live in a community property state, you will be required to provide additional information regarding your spouse’s income. ( Community property states: AZ, CA, ID, LA, NV, NM, TX, WA, WI)
If you are using online TurboTax to prepare your returns, you will need to prepare two separate returns and pay twice since with online, you get one return per fee.
If you are legally married as of 12/31/2025 then you should be filing as Married Filing Jointly and claim all of the children as dependents. When married and living together it is immaterial whether you or your spouse is the biological parent of the child being claimed as a dependent.
Usually, joint filing is better. But the only way to know for sure is for you to compare it both ways. We can't help you with whether filing jointly will impact your daughter's eligibility for a special health care program. (Adding income might make you less eligible, but having a larger family size/more kids might counteract that.) You have to ask the program.
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