What bookkeeping does a small nonprofit need to file Form 990?

Excite Tax's answer for Utah nonprofits: the Form 990 version you file sets the books; a group with receipts normally $50,000 or less may file the e-Postcard, and churches are exempt.

Short answers

What are the alternatives for keeping a nonprofit's books?

Four common ones: a volunteer treasurer with a spreadsheet, a volunteer with accounting software, a paid part-time bookkeeper, or an outside bookkeeping service. Excite Tax's view is that any of them works if a second person reviews the bank reconciliation every month and the system can tag restricted gifts and split expenses by function. The trade-offs are below.

What makes nonprofit bookkeeping different

Bookkeeping for nonprofits is ordinary double-entry bookkeeping with three extra tags on each transaction: whether a donor restricted the money, which function spent it, and who gave it. The IRS compliance guide for charities says the books must show gross receipts, purchases, expenses, employment taxes and assets, and that a charity with more than one program should keep records that identify the income and expenses of each.

Which return your nonprofit files

The return is chosen by size, and the size comes straight from the books.

Which annual return, by size (the IRS Form 990 series chart, and the church exception in the Code)

Your organisationReturn
Gross receipts normally $50,000 or lessForm 990-N, the e-Postcard, or a full return by choice
Gross receipts under $200,000 and total assets under $500,000Form 990-EZ or Form 990
Gross receipts of $200,000 or more, or total assets of $500,000 or moreForm 990
A private foundation, at any sizeForm 990-PF
A church, its integrated auxiliaries, or a convention or association of churchesNo annual return required

"Normally" has a precise meaning for the e-Postcard: a group in its first year qualifies with $75,000 or less received or pledged, a group between one and three years old with an average of $60,000 or less over its first two years, and an older group with an average of $50,000 or less over the last three years, the current year included. Gross receipts are everything received from all sources, without subtracting any costs or expenses.

A worked example

A made-up Utah youth soccer league, four years old, on a calendar year. Its gross receipts were $38,000 in 2023 and $52,000 in 2024. In 2025, registrations and sponsorships bring in $31,000, and a spring gala sells $30,000 of tickets and auction items against $12,000 of food, venue and prize costs, all of it counted before costs.

The e-Postcard test for the made-up league (a three-year average, the current year included)

YearGala booked grossGala booked net
2023 gross receipts$38,000$38,000
2024 gross receipts$52,000$52,000
2025 gross receipts$61,000$49,000
Three-year average$50,333$46,333
e-Postcard allowed at $50,000 or lessNoLooks like yes

Booked gross, the league is over the line and owes Form 990-EZ or Form 990 for 2025. Booked net, the same league looks eligible for the e-Postcard and files the wrong return, and netting contributions against fundraising costs is the example of incorrect information the penalty instructions give. The $12,000 of gala costs still belongs in the books, as direct expenses of the fundraising event on the full return.

Split every expense by function

This is the part most small nonprofits' books cannot produce on demand. On the full return, section 501(c)(3) and 501(c)(4) organizations must complete all four columns of Part IX: total, program services, management and general, and fundraising. If the accounting system does not allocate expenses, any reasonable method may be used, but the method must be documented in the records.

A worked example

The instructions give the rule in one example: an employee who spends 40% of the time on fundraising and 60% on program management is allocated 40% and 60%, not 100% to programs. Applied to a made-up executive director paid $48,000 who keeps a timesheet for a sample of weeks, with the method written down:

A made-up director's $48,000 salary, split by time (the Form 990 allocation rule)

FunctionShare of timeAmount
Program services60%$28,800
Management and general25%$12,000
Fundraising15%$7,200

Excite Tax's view: set the split once a year from a sample of timesheets or calendars, write the method down in a one-page memo, and post it each month with a journal entry. The books then hold the columns before anyone starts the return, and the same memo covers rent, software and insurance.

Restricted gifts and net assets

A donor restriction can be a time restriction, a purpose restriction or both, and the balance sheet reports net assets with donor restrictions separately from net assets without them. A board designation is not a donor restriction: funds without a donor-imposed restriction stay on the without-restrictions line whatever the board sets aside.

In the books, that means a class, fund or tag on every restricted grant from the day it is deposited, and an entry releasing it when the money is spent on the named purpose. Without the tag, a $20,000 grant for a new program sits in the bank balance looking like money without donor restrictions, and the board can spend it twice.

Donations, receipts and events

Events are where gifts and sales mix. The instructions' own example: a $400 ticket to a dinner with a retail value of $160 is a $160 purchase and a $240 contribution, and the two parts are recorded separately. Because the $400 payment is more than $75, the ticket also needs a disclosure statement. Once event contributions and event income together exceed $15,000, the return adds Schedule G, Part II.

Churches: no annual return, but still books

Section 6033(a)(3)(A)(i) of the Internal Revenue Code excuses churches, their integrated auxiliaries, and conventions or associations of churches from the annual return, so a church files neither the e-Postcard nor the full return. That is not the same as needing no books. Donors still need acknowledgments for gifts of $250 or more, unrelated business income of $1,000 or more still means Form 990-T, and a church with staff still runs payroll. Utah's annual filing does not apply to an organisation the IRS does not require to file.

A nonprofit bookkeeping guide, month by month

  1. Open a bank account in the organisation's name and run every dollar through it. The IRS guide says the checkbook may be the main source for the books of most small organisations, which only works if nothing bypasses it.
  2. Set up a chart of accounts with contributions, grants, program revenue and event revenue as separate income lines, and a function tag (program, management and general, fundraising) for expenses.
  3. Tag each restricted gift to its fund when it is deposited, and release it when it is spent on the purpose.
  4. Record deposits at the full amount and event costs and card fees as expenses, because gross receipts are measured before costs.
  5. Keep the donor list current and send acknowledgments as gifts arrive, not in a January rush.
  6. Reconcile every bank and card account monthly, with a second person, a board member who does not sign checks, reviewing it; see what a bank reconciliation is.
  7. Post the month's functional split with a journal entry from the written allocation memo.
  8. At year end, total the gross receipts and total assets and check them against the Form 990 series thresholds before choosing the return.
  9. File by the 15th day of the 5th month after the year ends, May 15 for a calendar year, or file Form 8868 for an automatic 6-month extension.

Cash or accrual both work. A charity chooses its accounting method when it files its first annual return, and under an accrual method a pledge is recorded as income in the year it is received, even if it is paid later. The difference is explained in cash vs. accrual accounting, and the monthly routine in the month-end close checklist.

Deadlines, and what missing them costs

Form 990 is due on the 15th day of the 5th month after the accounting period ends, and the e-Postcard keeps the same calendar and cannot be filed until the year is over. Form 8868 requests an automatic 6-month extension of time to file.

Late costs money on the full return. For a 2025 return, the penalty is $25 a day, up to the lesser of $13,000 or 5% of gross receipts, and $130 a day, up to $65,000, once gross receipts exceed $1,309,500. The e-Postcard has no late-filing penalty, but three consecutive years without a required return revoke the exemption automatically, on the due date of the third.

The alternatives: who keeps the books

Nonprofit bookkeeping alternatives, and what to check with each

OptionWorks whenWatch for
A volunteer treasurer with a spreadsheetA group that files the e-Postcard, with few transactions and no restricted grantsNo audit trail, and the books leave when the treasurer does
A volunteer with accounting softwareRestricted gifts or several programs, with a treasurer who reconciles monthlyTurnover: write down the chart of accounts and the allocation memo
A paid part-time bookkeeperPayroll, grants that require reports, or a full returnOne person handling deposits, payments and the reconciliation
An outside bookkeeping serviceA board that wants monthly statements without hiring an employeeWhether the service splits expenses by function and tracks donor restrictions

Excite Tax's answer, whichever you choose: separate the duties. The person who reconciles the bank should not be the only person who signs checks, and the board should see a statement of activities and a balance sheet every quarter; see do I need a balance sheet and how to choose a bookkeeper.

If the books are years behind, the rebuild order in two years behind on bookkeeping applies to a nonprofit too; start with the bank statements and the donor list.

Records to keep, and for how long

What a receipt or a deposit record has to show is covered in what records the IRS requires and do I need to keep receipts.

In Utah

shall annually file with the Division of Corporations and Commercial Code an unredacted copy of ... most recently filed IRS Form 990, 990-EZ, 990-N, or 990-PF.
Utah Code § 13-22-110, Financial reports required -- Rulemaking (effective May 6, 2026)

In plain words: a Utah nonprofit corporation, or a foreign nonprofit corporation, files an unredacted copy of its most recently filed 990, 990-EZ, 990-N or 990-PF with the Division of Corporations and Commercial Code every year, and a full return for a year more than three years back does not count. The division may not require Schedule B, and Form 990-T is not required. A new charity with no return yet may file its IRS determination letter instead, if the letter is dated no more than two years back.

The Department of Commerce describes the same duty: since January 1, 2025, nonprofits doing business in Utah register the entity with the Division of Corporations and Commercial Code and upload the latest federal return each year. The Charitable Solicitations Act's registration now falls on professional fundraisers and professional fundraising consultants. A charity that hires one should know the deposit rule: the fundraiser deposits each contribution into an account in the charity's name within 10 days, and the charity has sole control of withdrawals.

For the books, the Utah filing is the federal return filed a second time, so the work is the same work. Keep the accepted return and the filing confirmation with the year's records.

When to hand this to a preparer

Hand the books over when keeping them costs more hours than the business can spare, or when they stop agreeing with the bank.

Nonprofit bookkeeping is not a service Excite Tax lists yet; bring these records to whoever prepares the organisation's annual return.

Sources

  1. IRS, Form 990 series: Which forms do exempt organizations file (page updated June 28, 2026) · retrieved September 2026
  2. IRS, Annual electronic filing requirement for small exempt organizations — Form 990-N (e-Postcard) (page updated June 27, 2026) · retrieved September 2026
  3. 26 U.S. Code § 6033, Returns by exempt organizations (LII, Cornell Law School), subsection (a)(3)(A)(i) · retrieved September 2026
  4. IRS, Instructions for Form 990, Return of Organization Exempt From Income Tax (2025) · retrieved September 2026
  5. IRS, Instructions for Schedule B (Form 990) (12/2024), Schedule of Contributors · retrieved September 2026
  6. IRS, Charitable contributions: Written acknowledgments (page updated June 28, 2026) · retrieved September 2026
  7. IRS, Unrelated business income tax (page updated June 27, 2026) · retrieved September 2026
  8. IRS, Automatic revocation of exemption (page updated June 28, 2026) · retrieved September 2026
  9. Utah Code § 13-22-110, Financial reports required -- Rulemaking (effective May 6, 2026) · retrieved September 2026
  10. Utah Code § 13-22-104, Registration required (effective May 6, 2026) · retrieved September 2026
  11. IRS, Publication 4221-PC (Rev. 3-2018), Compliance Guide for 501(c)(3) Public Charities, Recordkeeping · retrieved September 2026
  12. IRS, Charitable contributions: Quid pro quo contributions (page updated June 28, 2026) · retrieved September 2026
  13. IRS, Instructions for Form 8868 (01/2026), Application for Extension of Time To File an Exempt Organization Return · retrieved September 2026
  14. Utah Department of Commerce, Division of Consumer Protection, Charities: Annual Filing Requirements with the Utah Division of Corporations · retrieved September 2026
  15. Utah Code § 13-22-111, Separate accounts and receipts required (effective May 6, 2026) · retrieved September 2026

Ranked and explained on the sources page.