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Nonprofit Year-End Checklist: How to Prepare for IRS Form 990 Filing

Jul 10, 2026 10:02:01 AM Kathy Dise QuickBooks, Financial Management, For Accountants, Record Keeping, Non Profit Finance, Year End Accounting, nonprofit accounting, board reporting, nonprofit 990 preparation, Nonprofit Tax Filing, Nonprofit Financial Reporting, Nonprofit Financial Statements, Foundation Accounting, Functional Expense Allocation, Nonprofit Best Practices, Year End Checklist, Form 990, Nonprofit Finance Management, Nonprofit Audit Preparation, Charitable Organizations, Tax Exempt Status, IRS Compliance, IRS Form 990, 501(c)(3) Organizations, Tax Exempt Organizations, Nonprofit Bookkeeping, Donor Reporting, Grant Accounting, Nonprofit CFO Services, Nonprofit Financial Planning

Nonprofit Year-End Checklist: How to Prepare for IRS Form 990 Filing
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Non profit 990 filing blog

What is a 990?

A Form 990 is the IRS-required tax return for nonprofits—and yes, it’s public. Think of it as your organization’s financial highlight reel. Donors, watchdogs, and curious supporters use it to see how responsibly you’re spending and whether your mission matches your money.

Do I need to File a 990?

If you’re a nonprofit, the odds are: yes. Annual filing applies to many organizations, including:

Common Filers

  • 501(c)(3) charities (public charities & foundations)
  • 501(c)(4) social welfare organizations
  • 501(c)(5) labor unions
  • 501(c)(6) trade associations
  • 501(c)(7) recreational clubs
  • 501(c)(15) small insurance groups
  • Section 527 political organizations
  • How many people are employed for the Fiscal Year(FY)?
  • Key personnel: names, titles, compensation and benefits
  • Officers and Board members – Any changes- include Name, title, addresses and hours worked. Note if voting or non-voting
  • Donors giving $5,000+ (name, address, amount)
  • Non-cash / in-kind donations
  • Functional expense allocation (Program, Fundraising, Admin)
  • Prior Year 990 diling
  • Statement of Financial Position (Balance Sheet)
  • Statement of Activity (P&L)
  • Trial Balance
  • General Ledger (detailed)
  • Bank & investment statements
  • W-2s and W-3
  • 1099 NEC, MISC and 1096 filing documentation

Skipping it isn’t just risky—it can cost you your tax-exempt status. Yikes.

Your Year-End 990 Prep Checklist

Before your CPA starts asking questions (they will), gather this:

Key Organizational Info

Donor & Contribution Details

Financial Breakdown

The Functional Expense Worksheet classifies your expenses into Program, Fundraising, and Administrative categories using your Statement of Activity. Expenses are allocated based on how they support each function, often using percentages for shared costs like salaries or overhead. This breakdown helps demonstrate how resources are used, with a common benchmark of 65–75% of total expenses directed toward program activities to reflect strong mission alignment.

Financial Documents

Final Thoughts

A clean, accurate 990 tells your story—and builds trust faster than any marketing campaign. If your records feel… less “organized” and more “creative chaos,” now’s the time to act.

Contact BudgetEase today—because your 990 is already public… let’s make sure it’s also impressive.

Kathy Dise

Written by Kathy Dise

Kathy has over 30 years experience helping small businesses succeed. As a commercial lender, commercialization expert and now as a QuickBooks diamond level advisor, Kathy understands the challenges small business owners face. Her experience helps business owners quickly accomplish their financial goals. As the owner of BudgetEase, Kathy works with clients to develop a plan to efficiently process 1,000s of small transactions so owners can make informed decisions. She lives in Shaker Heights, OH with her husband Ralph and enjoys golf, curling and walking in Cleveland’s fabulous Metro Parks.