Yes, you can file it with only the Schedule C and enter the housing allowance when asked. There are steps for a W-2 however it would still require the EIN and name of church. The church should expect that you would need an EIN however the Schedule C will allow you to file without it.
The IRS may inquire later as to why the Schedule C has no income and you can explain at that time. The church should be issuing a W-2 even if the only entry is Box 14 with your housing allowance. A minister is a 'common law' employee of the church.
Who is a Minister? IRS Topic 417
According to the IRS, ministers are individuals who are duly ordained, commissioned, or licensed by a religious body constituting a church or chard denomination. They are given the authority to conduct religious worship, perform sacerdotal functions, and administer ordinances or sacraments according to the tenets and practices of that church or denomination. If a church or denomination ordains some ministers and licenses or commissions others, anyone licensed or commissioned must be able to perform substantially all the religious functions of an ordained minister to be treated as a Minister for Tax Purposes. See publication 517
Ministers have a dual-tax status. For federal income taxes they ordinarily are employees, however for Social Security they are self-employed with regard to services performed in the exercise of their ministry.
IRS FAQs Housing Allowance The housing allowance is usually shown in box 14 of the W-2, not always listed.
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