Employers should not file a 1099 form for payments sent to a tax-exempt nonprofit organization. Check to confirm that any business you sent a payment to qualifies under one of the types of exempt organizations. There are situations when you may still need to send out a 1099 form.
A nonprofit that does business with other nonprofits must still fill out a 1099 for their own:
- Vendors
- Independent contractors
- Attorneys
- All other applicable parties
Filing requirements relate to your business’s transactions and the overall legal structure. The Internal Revenue Service requires many nonprofits to fill out 990s as well. Others who must submit 990s are:
- Tax-exempt organizations
- Nonexempt charitable trusts
- Section 527 political organizations
Exemptions for the form include some government corporations and faith-based organizations.
People Also Ask
- What 1099 forms do nonprofits typically file each year? – A nonprofit might file a 1099-NEC and/or a 1099-MISC. Filing a 1099-NEC is most common for when a nonprofit pays its independent contractors. Sending 1099-MISCs will occur if the nonprofit needs to report rent, prizes, awards, and/or legal settlements.
- Should nonprofits report reimbursements on a 1099 form? – The short answer is, sometimes. You do not need to report accountable plan reimbursements with the receipts. Alternatively, use a 1099-NEC to report flat stipends or non-accountable reimbursements.
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This article was updated on Dec. 20, 2025 to keep its information as fresh as possible. We update this article every six months, before and after tax season, to keep it current with any changes.