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Industry-Specific

Non-Profit Compliance Checklist

Alan Balmer, CPA
January 15, 2024
8 min read

Form 990, exempt status maintenance, record retention, and compliance best practices for 501(c)(3) organizations.

Table of Contents

Why Compliance Matters

Non-profit organizations face unique compliance requirements. Failure to file required forms can result in automatic revocation of tax-exempt status — and reinstatement is expensive and time-consuming.

Annual Filing Requirements

Form 990 (Return of Organization Exempt From Income Tax)

Who files: Organizations with gross receipts ≥ $200K or total assets ≥ $500K.

Due date: 15th day of the 5th month after fiscal year end (May 15 for calendar-year organizations).

Key sections:

  • Part I — Revenue, expenses, and net assets
  • Part III — Program service accomplishments
  • Part IV — Checklist of required schedules
  • Part VI — Governance, management, and disclosure
  • Part VII — Compensation of officers, directors, and key employees

Form 990-EZ (Short Form)

Who files: Organizations with gross receipts < $200K and total assets < $500K.

Due date: Same as Form 990.

Form 990-N (e-Postcard)

Who files: Organizations with gross receipts normally ≤ $50K.

Due date: Same as Form 990.

Note: If you fail to file for three consecutive years, your exempt status is automatically revoked.

Exempt Status Maintenance

Organizational Requirements

  • Operate exclusively for exempt purposes (charitable, educational, religious, etc.)
  • No private benefit to insiders
  • Limited lobbying activities
  • No political campaign intervention

Public Charity vs. Private Foundation

Most organizations want to be classified as public charities (not private foundations) because:

  • Higher deduction limits for donors
  • Less restrictive investment rules
  • No excise tax on investment income

Public support test: You must receive at least 33⅓% of support from the general public, government, or other public charities (not from gross receipts, interest, or dividends).

Record Retention

Non-profits should retain:

  • Formation documents — Articles of incorporation, bylaws, exempt status determination letter (permanently)
  • Governance records — Board minutes, conflict of interest policies, whistleblower policy (permanently)
  • Financial records — Bank statements, invoices, receipts (7 years)
  • Donor records — Acknowledgment letters for contributions ≥ $250 (7 years)
  • Employment records — Payroll, W-2s, I-9s (7 years after termination)

Unrelated Business Income Tax (UBIT)

If your organization earns income from a trade or business that is not substantially related to your exempt purpose, you may owe UBIT.

Common triggers:

  • Rental income from mortgaged property (debt-financed income)
  • Advertising revenue
  • Revenue from activities not related to exempt purpose

Filing: Form 990-T if gross unrelated business income ≥ $1,000.

State Compliance

In addition to federal requirements, most states require:

  • Annual report filing with secretary of state
  • State tax exemption application (separate from IRS)
  • Solicitation registration (if fundraising)
  • Sales tax exemption (for purchases, not sales)

Compliance Checklist

  • ☐ File Form 990/990-EZ/990-N annually by deadline
  • ☐ Maintain organizational documents (articles, bylaws, determination letter)
  • ☐ Hold regular board meetings and document minutes
  • ☐ Adopt and enforce conflict of interest policy
  • ☐ Provide donor acknowledgment letters for contributions ≥ $250
  • ☐ File state annual reports
  • ☐ Maintain state tax exemption
  • ☐ Register for solicitation (if fundraising)
  • ☐ Monitor unrelated business income
  • ☐ Retain records per retention policy

Next Steps

Non-profit compliance is complex, but critical. Alan has decades of experience serving as financial controller for a national non-profit. He provides ongoing compliance guidance, public charity classification consulting, and — when needed — full controller-level financial management.

Key Takeaways

  • S-Corp elections can save $3K-$15K+ annually in self-employment taxes
  • You must pay yourself a "reasonable salary" before taking distributions
  • S-Corp status is ideal for business owners earning $40K+ in net income
  • File Form 2553 by March 15 to elect S-Corp status
  • Work with a CPA to determine the right salary vs distribution split
Alan Balmer, CPA

Alan Balmer, CPA

Alan Balmer is a licensed CPA with 25+ years of experience helping Texas business owners optimize their tax strategy. He's filed 10,000+ returns and saved clients over $100M in taxes through strategic planning and entity structuring.

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Schedule a consultation with Alan to discuss your specific situation and discover how much you could save.

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