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Parsonage allowance Ministers can exclude from their income a rental allowance or the fair rental value of a parsonage that is provided to them as pay for their services. This exemption applies only for income tax purposes. The exclusion does not apply to self-employment taxes.
California Tax Filing Requirements for Churches FTB 199N (California e-Postcard) Form 199 (Exempt Organization Annual Information Return) Form 109 (Exempt Organizations Business Income Tax Return) Form 100 (Corporation Franchise or Income Tax Return)
A tax-exempt organization must file required information returns, such as Form 1099-MISCPDF. An organization does not withhold income tax or social security and Medicare taxes from, or pay social security and Medicare taxes or federal unemployment tax on amounts it pays to an independent contractor (non-employee).
For services in the exercise of the ministry, members of the clergy receive a Form W-2 but do not have social security or Medicare taxes withheld. They must pay social security and Medicare by filing Schedule SE (Form 1040), Self-Employment Tax.
For the most part, ministers are deemed to be common-law employees of the religious organization for which they work, and thus they should receive a W-2 form. There are only a limited number of instances where a 1099-MISC may be applicable, one of which is if a minister is a traveling evangelist.

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The answer is both. Ministers have what is commonly referred to as dual tax status. For federal income tax purposes, a minister is generally treated as a common-law employee. For payments into Social Security, the minister is always self-employed. This is an IRS regulation and not an election.
Employee or Self-Employed Generally, youre an employee if the church or organization you perform services for has the legal right to control both what you do and how you do it, even if you have considerable discretion and freedom of action.
Churches and religious organizations are generally exempt from income tax and receive other favorable treatment under the tax law; however, certain income of a church or religious organization may be subject to tax, such as income from an unrelated business.
There are versions of the 1099 to report payments for services as well as interest, dividends, and real estate sale proceeds. This form is issued by churches to guest speakers, pulpit supply, etc., who provide services in excess of $600. Churches generally dont withhold taxes from the payments to these workers.
While they can be considered an employee of a church, for federal income tax purposes a pastor is considered self-employed by the IRS. Some pastors are considered independent contractors if they arent affiliated with one specific church, like traveling evangelists.

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