The single audit: thresholds, timing, and how to prepare

A single audit is an annual audit that covers both your financial statements and your compliance with federal award requirements. It's called "single" because one audit satisfies all your federal funders at once, instead of each agency auditing you separately. The rules are in Subpart F of the Uniform Guidance (2 CFR 200.500–200.521).

For a nonprofit crossing the threshold for the first time, the single audit is a step up in cost, effort, and scrutiny. Organizations that prepare well usually come through cleanly. Organizations that discover the requirement in month ten of the fiscal year usually don't. This guide covers when you need one, what counts, what it involves, how to choose an auditor, and how to handle findings. It reflects the rules as of October 2026. Your auditor is the final word on how they apply to you.

Do you need one?

Under 200.501, a nonprofit that expends $1,000,000 or more in federal awards during its fiscal year must have a single audit (or, in limited cases, a program-specific audit). The 2024 Uniform Guidance revisions raised the threshold from $750,000, effective for fiscal years beginning on or after October 1, 2024.

So for a nonprofit on a calendar fiscal year, the $1,000,000 threshold first applied to fiscal year 2025 (January 1, 2025 start). For a July 1 fiscal year, it first applied to the year starting July 1, 2025.

If you spend less than the threshold, you're exempt from Subpart F audit requirements for that year, but your records must still be available for review by the agency, pass-through entity, and GAO, and your funders may still require a financial statement audit by contract.

Program-specific audits

If you expend federal awards under only one federal program (not research and development) and the program's rules don't require a financial statement audit, you may be able to choose a program-specific audit instead (200.501(c) and 200.507). Few nonprofits qualify. Ask your auditor.

What counts as "federal awards expended"

This is where nonprofits most often miscalculate. Under 200.502, the determination is based on when the activity related to the award happens, not when you get the cash. Federal awards expended include:

• Expenditures and expenses under grants, cooperative agreements, and cost-reimbursement contracts
• Disbursements to your subrecipients (if you're a pass-through entity)
• The use of loan proceeds under federal loan programs, plus certain prior-year loan balances with continuing compliance requirements
• The receipt of federal property or surplus property
• The receipt or use of program income
• Certain other federal assistance, such as noncash assistance

What matters for nonprofits in practice:

• Pass-through money counts. Federal funds you receive from your state, county, city, or another nonprofit count exactly like direct federal grants. A state "workforce grant" or "victim services grant" is often federal money. Check the subaward for an Assistance Listing number.
• Multi-year awards count by year of spending. A $1.5 million three-year award spent at $500,000 a year contributes $500,000 a year.
• Contracts for goods or services you sell to a government (where you're a contractor, not a subrecipient) generally don't count. The distinction is in 200.331. See subawards and pass-through funding.
• Cost share you contribute isn't federal expenditure.

What the single audit involves

A single audit has more parts than a standard financial statement audit:

1. Financial statement audit under Government Auditing Standards ("Yellow Book")
2. Schedule of Expenditures of Federal Awards (SEFA), which you prepare, listing every federal program, Assistance Listing number, pass-through entity and identifying number, and amount expended, plus amounts passed through to subrecipients
3. Internal control and compliance testing of your major programs, selected by the auditor using a risk-based approach (200.518). Larger programs are "Type A," and the Type A threshold for most entities starts at $1,000,000
4. Auditor's reports on financial statements, internal control, compliance, and the SEFA
5. Schedule of findings and questioned costs
6. Your summary schedule of prior audit findings and corrective action plan (200.511)

The auditor tests major programs against the OMB Compliance Supplement, which lists the compliance requirements for each major federal program: activities allowed, allowable costs, cash management, eligibility, equipment, matching, period of performance, procurement, program income, reporting, subrecipient monitoring, and special tests. OMB updates the Supplement each year. As of mid-August 2026, the 2026 Supplement hadn't yet been released, and auditors can't issue final single audit reports for affected years until it is. The 2025 edition was issued in November 2025, later than OMB had planned, so build some slack into your timeline.

The timeline and the FAC

Under 200.512, you must submit the audit, the data collection form, and the reporting package within 30 calendar days after you receive the auditor's report, or nine months after the end of the audit period, whichever is earlier.

Remember the 30-day rule: if your auditor delivers the report in month five, your deadline is month six, not month nine.

Filing at FAC.gov

Single audits are filed with the Federal Audit Clearinghouse at FAC.gov, operated by the General Services Administration. GSA launched it in October 2023, replacing the older Census Bureau system, and it uses Login.gov for sign-in. Under 200.512, the FAC is the repository of record. Federal agencies and pass-through entities get your audit from the FAC rather than from you.

The submission typically involves:

• Completing the data collection form (the SF-SAC information, now entered in FAC.gov), including your SEFA data and findings
• Uploading the reporting package as a single PDF
• Certification by the auditee (an authorized official from your organization) and by the auditor

Audits submitted to the FAC are publicly available, generally including your financial statements and findings, so write your corrective action plan with that in mind.

Choosing and working with an auditor

Not every CPA firm does single audits, and the quality gap between firms is real.

Procure the auditor properly. Under 200.509, you must procure audit services following the Uniform Guidance procurement standards and your own procurement policy. For most nonprofits that means requesting proposals from more than one qualified firm.

What to look for:

• Experience with nonprofit single audits, ideally with programs like yours
• A current peer review, required for firms performing audits under Government Auditing Standards. Ask for the most recent peer review report
• Staff with the required Government Auditing Standards continuing education
• Membership in the AICPA's Governmental Audit Quality Center is a positive signal, though not required
• Clear fees and a realistic timeline that meets your FAC deadline

One restriction: an auditor who prepares your indirect cost proposal or cost allocation plan may not audit you if indirect costs you recovered in the prior year exceeded $1 million (200.509(a)).

Rotation isn't required by the Uniform Guidance, but many boards seek new proposals every five or so years to test price and quality.

Getting ready: a year-round plan

Single audit preparation is mostly a year-round habit of good grant accounting.

At the start of the fiscal year:

• Identify all federal funding, including pass-through, and estimate expenditures
• Get every award document, subaward agreement, and amendment into one folder per award
• Confirm the Uniform Guidance version, indirect rate, and special conditions for each award
• Talk to your auditor about likely major programs

Every month:

• Reconcile grant expenditures to the general ledger
• Keep time and effort records current
• Document procurement decisions as they happen
• File financial and performance reports on time, and keep copies

Before fieldwork:

• Prepare a draft SEFA, reconciled to your general ledger and to funder reports
• Gather documentation for a sample of transactions per major program (invoices, approvals, timesheets, quotes)
• Assemble subrecipient monitoring files, if you're a pass-through entity
• Update the status of prior findings

Audit findings: what they are and how to respond

Under 200.516, auditors must report, among other things:

• Significant deficiencies and material weaknesses in internal control over major programs
• Material noncompliance with federal requirements
• Known or likely questioned costs greater than $25,000 for a type of compliance requirement for a major program
• Known or likely fraud affecting a federal award

Common nonprofit findings include missing time and effort documentation, procurement without required quotes, late or inaccurate financial reports, SEFA errors, inadequate subrecipient monitoring, and charging costs outside the period of performance.

Responding well

For each finding, you prepare a corrective action plan (200.511) naming the responsible person, the planned actions, and the completion date. If you disagree with a finding, say so and explain why.

The awarding agency or pass-through entity then issues a management decision on each finding, generally within six months of the audit's acceptance by the FAC (200.521). Respond promptly to requests for information. Unresolved findings carry into next year's summary schedule of prior findings and can affect your risk rating.

Low-risk auditee status

If you've had single audits for each of the two previous years, submitted them on time, received unmodified opinions, and had no material weaknesses or major-program findings above certain levels, you may qualify as a low-risk auditee (200.520). That lets the auditor test a smaller share of your federal spending, which usually means a smaller, cheaper audit. Filing late can cost you that status.

When you're a subrecipient

If you get federal funds through a state or another pass-through entity, that entity must verify that you've had a single audit when required, and it will follow up on findings related to its subaward (200.332). Expect to be asked:

• Whether you expect to exceed the threshold this year
• For a link to your FAC submission
• For your corrective action plan on any findings related to its funds

Answer promptly. Pass-through entities factor your audit results into their risk assessment and monitoring.

Board responsibilities

Your board, usually through an audit or finance committee, should:

• Approve the auditor selection after a competitive process
• Meet with the auditor at the start and end of the audit, including without staff present
• Review findings and approve the corrective action plan
• Track that corrective actions are completed

See the board's role in grants.

Single audit checklist

• All federal funding identified, including pass-through, with Assistance Listing numbers
• Expenditures projected against the correct threshold for your fiscal year
• Auditor procured under 200.509, with current peer review and single audit experience
• SEFA reconciled to the general ledger and funder reports
• Documentation ready for major programs
• FAC.gov access tested for your certifying official
• Deadline calculated (30 days after report, or nine months after year-end, whichever is earlier)
• Corrective action plans written for any findings, with owners and dates
• Board reviewed the audit and findings

For the rules your auditor will be testing, see our Uniform Guidance guide and post-award compliance.