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Any company (non-profit or not) can reimburse employee expenses under one of two plans.
1. An accountable plan -- you are only reimbursed for actual qualifying expenses and you must submit receipts to the company to prove your expenses. Accountable reimbursements are not taxable, and can't be used for a tax-deduction since the money was never taxed in the first place (double dipping).
2. A non-accountable plan -- the company can pay anything they want; all or part of your expenses, or a flat rate, for qualified or non-qualified travel, and with or without receipts, but the reimbursements are taxable and must be included in your 1099-MISC or W-2. Since the reimbursements are taxable income, you are free to deduct qualified expenses under the usual rules, using form 2106 and schedule A. Since this is an itemized deduction subject to the 2% rule, your actual tax benefit will be reduced depending on your other tax facts.
Qualifying expenses for work-related travel are covered in publication 463. Generally, the travel must be (1) away from your tax home, and (2) temporary. You can deduct actual travel expenses, actual lodging expenses, and 50% of food or 50% of the meals per diem rate for the location you worked in. https://www.irs.gov/uac/about-publication-463
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