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The IRS's Audit Techniques Guide states on page 14: https://www.irs.gov/pub/irs-utl/ministers.pdf "Ministers often pay a small annual renewal fee to maintain their credentials, which constitutes a deductible expense. However, ministers' contributions to the church are not deductible as business expenses. They may argue that they are expected to donate generously to the church as part of their employment. This is not sufficient to convert charitable contributions to business expenses. The distinction is that charitable contributions are given to a qualifying organization (such as a church) for the furtherance of its charitable activities. Dues, on the other hand, are usually paid with the expectation that a financial benefit will result to the individual, as in a realtor's multi-list dues or an electrician's union dues. A minister's salary and benefits are not likely to directly depend on the donations made to the church. They may still be deducted as contributions on Schedule A but may not be used as a business expense to reduce self employment tax."

https://www.clergyfinancial.com/are-mandatory-tithes-a-deductible-business-expense/

Rather than giving money back to her church, she can pay less social security by reducing the amount she receives from her church.

Sounds like deja vu all over again. I remember Arthur Andersen auditing companies that went kaput. Gave them clean audit reports. When I was young, I thought auditing was the thing. I never worked in a big firm but did audit work with a small firm auditing local government entities (school boards, cities, etc.). On my own, I audited some small non-profit organizations. I began to feel uneasy about the whole auditing function. I haven't done audit work in years but I am very skeptical about the whole thing. Maybe I'm just old and jaded. If I sound cynical, that's because I am.

That was a terrible decision. You make it sound like you persuaded him to do this. If so, that makes the decision even worse. You should have persuaded him to file an extension and wait. Live and learn. File extensions, they're your friend.