How to keep your Missouri Nonprofit Compliant

Once you form a 501(c)(3) Nonprofit Public Charity in Missouri, follow this guide to keep it in good standing.

(Read our guide to learn how to form a nonprofit in Missouri.)


1. Apply for exemption from state taxes

A. State Income Tax Exemption

Once your organization receives your 501(c) determination letter from the IRS, your nonprofit will automatically be exempt from state income taxes.


B. State Sales Tax Exemption

To determine if your organization is eligible for a sales tax exemption, access the Missouri Department of Revenue’s website. If eligible, you may fill out Form 1746 to apply for a sales and use tax exemption.

2. Annual Federal Returns for Tax-exempt organizations

A. Annual Federal Returns

Most tax-exempt nonprofit organizations are required to file an annual return with the IRS (Check the IRS website for a list of exceptions).

The annual gross receipt amounts for an organization determine which form should be used to file the annual federal return.

‘Gross receipt’ is defined by the IRS as “the total amounts the organization received from all sources during its annual accounting period, without subtracting any costs or expenses”

For gross receipts ≤$50,000 --- File 990-N
Gross receipts <$200,000 and total assets <$500,000 --- File 990- EZ
Gross receipts >$200,000 or Total assets >$500,000 --- File 990


For any questions, contact the IRS at

  • (800) 829-3676 (Form related questions)
  • (800) 829-1040 (general information)

FAQ

Q: When is form 990 due?
A: Form 990 is due on the 15th day of the 5th month after the taxable year of the organization comes to an end.

E.g. If the taxable year ends on Dec 31st, form 990 is due on May 15th.

NOTE: If an organization fails to file form 990 for 3 consecutive years, it will automatically lose tax-exempt status.


B. Unrelated Business Income

If an organization has a gross income of ≥$1000 from a trade or business that is not related to the stated purpose of the organization, then it must file Form 990-T to pay tax on that income.

If your organization expects to pay $500 or more for the year in taxes on unrelated business income, your organization must pay a quarterly estimated tax on the unrelated business income using Form 990-W.

3. Maintain a Registered Agent

Any nonprofit that has incorporated must have a registered agent who has an office address in Missouri. If your registered agent, or their office address, changes, you must file Form Corp. 59 either online or by printing and mailing the PDF version of the form to the Secretary of State so that your Articles of Incorporation may be updated. 

If you fail to notify the Secretary of State of this change, your corporation may be subject to termination.

4. File Periodic Reports

The Missouri Secretary of State requires nonprofits to submit a Corporate Registration Report, which is due each year by August 31st. Access the Missouri Online Business Filing System to file your report.

Failure to file the appropriate reports may subject your organization to termination.

5. Apply for Permits and Licenses

Missouri nonprofits do not need to obtain a general business license. You may, however, want to check with your city/county clerk’s office to determine if there are local requirements.

If you plan to host charitable gaming (bingo, raffles, etc.), you’ll need to obtain a gaming license through the Missouri Gaming Commission.

6. Charitable Registration

Charitable Missouri nonprofits are required to register with the Missouri Attorney General. You may submit the Initial Registration Statement through the Attorney General’s website

Your organization will also be required to submit an annual report each year, and you can also access the appropriate form on the Attorney General’s website.

7. Register with the Missouri Department of Revenue

If your nonprofit will have employees, you will need to register for withholding and unemployment insurance taxes with the Missouri Department of Revenue.

Registration is easy and can be completed online. You can also access contact details for the Department of Revenue.

8. Comply with Public Inspection Rules

To comply with federal regulations regarding 501(c)(3) charities, you will need to release the following documents to any member of the public that requests them:

  • Your organization’s annual returns for up to 3 years after the listed due date (including the following Forms: 990-PF, 990-EZ, 990-T, and 990)
  • Any supporting documents and attachments for the above 990 forms. However, you only need to include the nature of the contribution and the amount contributed for Schedule B.
  • Official IRS paperwork showing your organization is considered to be tax-exempt.
  • Your organization’s application for exemption and all supporting documents submitted with your application (including Form 1023).


Your organization does NOT need to share the following documents and information with members of the public:

  • Any portion of Form 990/990-EZ’s Schedule B that identify who contributors are.
  • Anything considered to be an unfavorable ruling, which can include previous denials of tax-exempt status.
  • Any additional information permitted to be withheld by the IRS, including things such as trade secrets, patents, etc.

Recommended: Inform your employees about their rights and stay compliant by posting labor law posters in your workplace.


FAQ

Q: Can I charge members of the public for copies?
A: Yes, you are permitted to request a reasonable amount to procure copies of requested documents.

Q: If requested, how much time do we have to produce the documents?
A:
It is ideal to produce these documents within the same working day. However, if your nonprofit has limited office hours due to the time of year, or you don’t have a physical office at all, you should produce the documents within 14 days.

Q: Do I actually need to provide physical copies of the requested documents?
A: If a member of the public as for copies of documents, whether in writing or in person, you are required to make them available.

NOTE: We recommend that nonprofits make these documents available on their website. That way, anyone who might request copies of these documents can simply head to your website to view and/or download them. This will help your organization remain compliant and save time dealing with these requests personally.

To learn more about forming a nonprofit, check out our How to Start a Nonprofit in Missouri guide.

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