Yes, you can obtain Health Insurance through the Marketplace and still qualify for the self-employed health insurance Deduction. See Publication 535 for more info here: https://www.irs.gov/publications/p535/ch06.html
You can deduct amounts you paid for medical insurance purchased through the
health insurance marketplace less any advance premium tax credit you received.
This deduction will be also be adjusted for any changes to your premium tax
credit made on Form 8962 when you file your tax return. The medical premium
amount will be reduced by any additional credit received or increased by any
premium tax credit repaid.
However, you do not have to enter the premiums you
paid out of pocket into the Medical Expense section of TurboTax. Instead just enter
your 1095-A into the Health Care section and TurboTax will automatically
apply the correct medical insurance premiums to Form 1040, line 29; self-employed health insurance deduction after your Form 1095-A is linked to your business, Schedule C.
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