Nonprofit Exempt Organizations may be exempt from income taxation, but not from the IRS or State taxing entities. Exempt organizations are generally required to file annual returns of the income and expenses for the nonprofit. (Do not forget your State filing!)
If a Nonprofit Exempt Organization has employees, it will be required to file returns and pay employment taxes. If a Nonprofit Exempt Organization has “independent contractors”, it may be required to file 1099 for the amount paid to that “Independent contractor”.
Unrelated business income will require an unrelated business income tax return. Unrelated business income is income derived from operating a “business” separate and apart from the nonprofit purpose and donations.
Some nonprofit exempt organizations are required by the IRS to file certain returns electronically.
Best practices: If your nonprofit exempt organization has sufficient money, hire a tax preparer/CPA to handle your tax matters. Insist that the person your hire send you confirmation that all the tax returns, federal and state, have been filed.