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Of course you can file a joint return. Any married couple can choose to file a joint return even if one or both are self-employed.
If you were legally married at the end of 2020 your filing choices are married filing jointly or married filing separately.
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 $24,800 (+$1300 for each spouse 65 or older) 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. Your limit for SALT (state and local taxes and sales tax) will be only $5000 per spouse. 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.
https://ttlc.intuit.com/questions/1894449-married-filing-jointly-vs-married-filing-separately
https://ttlc.intuit.com/questions/1901162-married-filing-separately-in-community-property-states
There is no reason from a tax standpoint for you to file anything other than Married Filing Jointly just because you are self-employed and you spouse is an employee who receives a W-2.
You will be entering your self-employment income and expenses on a Schedule C which is part of and included with the personal tax return, Form 1040.
Most pastors are not really self-employed, they are considered self-employed for income tax purposes, but if you work under the direction of an body that has authority to hire and fire you, set your compensation and working conditions, and so on (like a board of elders, or a bishop or representative of your denomination) then you are a common law employee and should receive a W-2 with your wages in box 1. (Boxes 2-6 should be blank because the church should not be withholding taxes.)
More information is here, https://go.efca.org/resources/document/preparing-tax-returns-clergy
In any case, it is almost always better for married spouses to file a joint return, even if your employment status is different.
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