Nonprofit bookkeeping services: what they include and what they cost
Nonprofit bookkeeping is the monthly work of recording transactions, reconciling accounts and tracking each grant and donor restriction so the year can be closed. It is not an audit, and the same firm should not do both. Across 16,036 Form 990 filings in our data the median reported accounting fee was $33,607 (IRS e-file, data as of 2026-09-20).
Last verified: 2026-09-20 · Every figure links its source.
What do nonprofit bookkeeping services include?
Bookkeeping is the recurring work that keeps the ledger usable: recording income and expenses, reconciling every bank and investment account, running payroll entries, coding each transaction to a program and a funding source, and tracking donor restrictions so the release of restrictions can be shown at year end. A nonprofit that spends federal money also needs its grant expenditures coded by Assistance Listing number all year, because the schedule of expenditures of federal awards is built from that coding (2 CFR 200.510).
- Monthly transaction coding by program, function and funding source
- Bank, investment and credit card reconciliations
- Accounts payable and receivable, and payroll journal entries
- Grant and contract tracking, including pass-through awards and subawards
- Donor restriction tracking and the release of restrictions
- Monthly or quarterly financial statements for the board and the finance committee
- Year-end close and the schedules the auditor will ask for
Source: 2 CFR 200.510 · Last verified: 2026-09-20
Bookkeeping vs outsourced accounting vs a CPA audit
These are three different purchases. Bookkeeping records what happened. Outsourced accounting adds the controller-level work: the chart of accounts, the close calendar, allocations and the financial package. An audit is an independent opinion on the finished statements, and the auditor must be independent of the accounting records under the government auditing standards that apply to a single audit (GAO Government Auditing Standards).
| Service | What you get | Who asks for it | Can the same firm audit you? |
|---|---|---|---|
| Bookkeeping | Transactions recorded and accounts reconciled | Internal, board, lender | No — the auditor cannot audit records it maintained |
| Outsourced accounting / controller | Close process, allocations, financial package | Board, funders | No, for the same reason |
| Form 990 preparation | The annual information return | IRS | Possible, with independence safeguards |
| Financial statement audit | An opinion on the statements | State charity law, funders, lenders | Yes — this is the auditor |
| Single audit | That opinion plus compliance testing of major federal programs | 2 CFR 200.501 once federal awards expended reach $1,000,000 | Yes |
The practical rule: one firm keeps the books, a different firm audits them. If a proposal offers both, ask in writing how independence is preserved before signing.
Source: GAO Government Auditing Standards · 2 CFR 200.501 · 2 CFR 200.509 · Last verified: 2026-09-20
How much do nonprofit bookkeeping services cost?
There is no public dataset of bookkeeping quotes, but Form 990 asks what the organization paid for accounting. Across 16,036 filings we parsed from the IRS e-file data, the reported accounting fee was $15,005 at the 25th percentile, $33,607 at the median and $73,358 at the 75th percentile. That line covers all accounting services bought in the year — bookkeeping, the audit, the 990 — so treat it as an upper bound for bookkeeping alone, not a quote.
| Measure | Amount | Basis |
|---|---|---|
| 25th percentile | $15,005 | 16,036 filings with a fee above zero |
| Median | $33,607 | same |
| 75th percentile | $73,358 | same |
What moves the number: transaction volume, the number of restricted funds and federal awards, payroll complexity, whether allocations are documented, and how clean the prior year was.
Source: IRS, About Form 990 · IRS Form 990 series downloads · Last verified: 2026-09-20
Can our bookkeeper also do our audit?
No, not the same firm doing both without safeguards that usually cannot be met in a small engagement. Preparing the records and then auditing them is a self-review, and the government auditing standards treat that as a threat to independence that must be eliminated or reduced to an acceptable level before the audit can be accepted. There is also a specific federal rule: an auditor who prepared the indirect cost proposal or cost allocation plan may not perform the single audit when indirect costs recovered in the prior year exceeded $1 million (2 CFR 200.509).
Source: GAO Government Auditing Standards · 2 CFR 200.509 · Last verified: 2026-09-20
What should a small nonprofit look for in a bookkeeping service?
- Fund accounting experience, not just small-business bookkeeping — ask how they track donor restrictions and how releases appear in the statements.
- Federal award experience if you receive grants: ask them to describe the schedule of expenditures of federal awards and what they need from you to keep it current.
- A written close calendar with a date the monthly package lands.
- Named staff, with backup, and a stated response time.
- Clean separation from whoever will audit you.
- A transition plan for the first 60 days, including the opening balances they will rely on.
Find a nonprofit CPA near me
Our directory is built from filed single audits, so it lists firms that have actually audited nonprofits rather than firms that advertise it: 1,770 firms appear as the auditor on three or more nonprofit single audits. Start with audit firms by state and narrow to your city, or read nonprofit accounting firms and CPAs for the full picture of who does what.
Source: Federal Audit Clearinghouse · Last verified: 2026-09-20
Questions and answers
What is the difference between nonprofit bookkeeping and accounting?
Bookkeeping records and reconciles transactions. Accounting adds the close process, allocations, financial statements and the judgment calls behind them. Many nonprofits buy both from one provider and call it outsourced accounting.
Can a bookkeeper prepare our Form 990?
Many do, and the Form 990 asks the organization to name its paid preparer. Preparing the return is separate from auditing the statements, and the audit must be done by an independent firm.
Related pages
Looking for an auditor rather than a bookkeeper? Find firms that audit nonprofits or post an audit RFP.
This is public-record information, not accounting or legal advice.