Nonprofit CPA in San Francisco, CA
Audits, grant accounting, internal controls and Form 990 support for San Francisco nonprofits managing multi-year grants, City contracts and boards that expect clear financial oversight.
Schedule a Consultation
Nonprofit CPA services for San Francisco organizations
A San Francisco nonprofit can sign a three-year foundation grant, renew a City department contract and close a capital campaign in the same quarter. Each arrives on a different schedule and with different strings: money received now for work in later years, reimbursements that land months after the expense, and pledges that count as revenue before the cash comes in.
Accounting for that correctly is most of the job, and it is what organizations usually need when they look for a nonprofit CPA in San Francisco. RTN CPA is a certified public accounting firm that serves nonprofit organizations, government agencies and districts, and small businesses. We help Bay Area nonprofits record grants in the right period, keep restricted money visibly restricted, and give their boards financial reports that support real oversight.
Audit work is led by Roman Richardson, CPA, who has more than 20 years of experience focused on nonprofit organizations and governmental districts. Tax work is led by Paul J. Stroub, CPA. We work with San Francisco organizations from our California offices.
Independent audits for Bay Area nonprofits
An audit is usually requested by someone outside the organization: a foundation, a City department, a lender or the board's audit committee. California also sets its own floor.
Charities registered with the California Attorney General must have their financial statements audited by an independent CPA for any fiscal year in which gross revenue reaches $2 million, not counting government grants the charity already accounts for to the funding agency (Government Code section 12586(e)). The audited statements must be available to the Attorney General and the public within nine months after year end.
- financial statement audits under nonprofit accounting standards
- Single Audits of federal awards (2 CFR 200, Subpart F)
- compliance audits required by a specific grant or contract
- reviews and compilations where a full audit is not required
- written recommendations on internal control findings
Multi-year grants are a common sticking point. Auditors look at whether each grant was recorded as conditional or unconditional, whether restrictions were released in the right period, and whether pledges receivable are supported. Settling those questions before fieldwork keeps fieldwork short.
We keep audit engagements separate from accounting and advisory work. Where RTN CPA already keeps an organization's books, prepares its statements or serves in a finance role, we review the AICPA independence requirements before agreeing to an audit. If those services would impair independence, the audit goes to another firm.
Multi-year & foundation grant accounting
Foundation grants in the Bay Area are often multi-year and come with conditions: a matching requirement, a milestone, or a report that must be accepted before the next installment. Under current nonprofit accounting standards, a grant with a barrier the organization must overcome and a right of return for the funder is conditional, and it is not recognized as revenue until the condition is met. An unconditional multi-year pledge is recorded when it is made and released from restriction over time. Mixing up the two distorts the financial statements and the board's picture of what is actually available to spend.
City funding adds another layer. The City and County of San Francisco coordinates fiscal and compliance monitoring of its nonprofit contractors through the Controller's Office, reviewing items such as the agency-wide budget, cost allocation plan, audited financial statements and fiscal policies. When federal money is involved, a Single Audit applies once federal award expenditures reach $1,000,000 in a fiscal year beginning on or after October 1, 2024.
- conditional and unconditional grant analysis
- multi-year pledge and restriction tracking
- grant budgets, match and reporting calendars
- federal award identification and SEFA preparation
- preparation for City fiscal and compliance monitoring
Form 990 & California filings
For a San Francisco nonprofit, Form 990 is often the first financial document a new foundation reads. For most charities, Part IX, the statement of functional expenses, shows how spending divides between program services, management and general, and fundraising. Those figures should agree with the audited financial statements rather than being rebuilt separately at filing time.
State filings follow the federal return. Registered charities generally renew each year with the Attorney General's Registry of Charities and Fundraisers on Form RRF-1, and exempt organizations generally file Form 199 or the 199N e-Postcard with the Franchise Tax Board. We prepare them together so the numbers match.
- Form 990, 990-EZ and 990-PF preparation
- Part IX functional expense reporting
- Form 990-T and unrelated business income review
- California Form 199 or 199N and RRF-1 coordination
- exempt-status and compliance questions
Accounting & internal controls
Board oversight depends on numbers the board can trust. That starts with basic controls: someone other than the bookkeeper reviews the bank reconciliations, approvals are documented, system access matches job duties, and grant expenses are coded when they are incurred rather than reclassified at year end.
Controls have to fit the size of the team. A five-person organization cannot separate every duty, so we look for compensating reviews that suit your staffing, such as a board treasurer who sees the bank statements each month. Day to day, our nonprofit accounting services cover the monthly close, fund accounting and functional expense allocation that make the audit and the 990 easier.
- monthly close and bank reconciliations
- fund and restricted net asset accounting
- functional expense allocation methods
- approval, access and segregation-of-duties review
- financial policies and procedures
- audit-ready schedules
Fractional CFO & long-term planning
Multi-year grants make long-term planning possible, and they make it necessary. When a large grant ends in year three, the board needs to know now what it was paying for and how that work will be funded afterward. Bay Area operating costs make the question sharper.
A fractional CFO or controller brings that planning into the organization without a full-time hire: multi-year budgets tied to grant terms, a reserve policy the board can adopt and measure, cash forecasts that account for reimbursement timing, and reporting that helps the finance committee ask better questions.
- multi-year budgets and grant runway planning
- operating reserve policies and targets
- cash flow forecasting
- finance committee and board reporting
- internal control design as the organization grows
Where Bay Area nonprofits run into trouble
These problems tend to surface at audit time, but they start much earlier in the year.
- Multi-year grants recorded as revenue all in year one, or not at all
- Restrictions released without documentation that the purpose or time period was met
- Functional expense allocations no one can explain
- City contract invoices that do not tie to the general ledger
- Boards receiving cash balances instead of budget-to-actual reports
- No plan for what happens when a large grant ends
Each of these can be fixed. The earlier in the year it happens, the less there is to rebuild when the auditors arrive.
What working with RTN CPA looks like
Every engagement begins with a conversation about your organization: revenue and funding sources, how many grants are active, who reviews the financial reports, and what deadlines are coming.
We confirm the scope in a written engagement letter, so it is clear whether the work is an audit, a review, accounting support or advisory. Across the firm, RTN CPA has more than 25 years of experience and has completed more than 100 audits.
- an initial call about your funding, systems and deadlines
- a written scope and engagement letter
- a clear document request list before work starts
- results explained to management and the board
We do not promise audit outcomes. We do tell you where the records stand before testing begins.
Find the right service
Go straight to the service you need:
Serving San Francisco and the Bay Area
We work with nonprofits in San Francisco and across the Bay Area, including the East Bay, the Peninsula and the South Bay, through secure file exchange and video meetings. RTN CPA also offers its services to nonprofits in these markets:
Talk with a San Francisco nonprofit CPA
If a multi-year grant is complicating your statements, a City monitoring visit is on the calendar, or the board wants better reporting, a short call is the best place to start.
Share your annual budget, funding mix and upcoming deadlines. We will suggest the type of engagement that fits and outline what it involves.
Questions San Francisco nonprofits ask
Does RTN CPA have an office in San Francisco?
No. RTN CPA is a California firm with addresses in Los Angeles and Roseville. We work with San Francisco and Bay Area nonprofits through secure file upload and scheduled phone or video meetings, and we discuss any in-person needs when we agree on the scope.
How should we account for a multi-year grant?
It depends on the terms. If the grant includes a barrier the organization must overcome and the funder has a right of return, it is conditional and is recognized as revenue only when the condition is met. If it is unconditional, the full promise is generally recorded when made and released from restriction as the time period or purpose is satisfied. We review the grant language with you before year end.
We have City contracts. What does fiscal monitoring involve?
The City and County of San Francisco coordinates fiscal and compliance monitoring of nonprofit contractors through the Controller's Office, and a nonprofit funded by several participating departments is generally monitored once rather than by each department. We can help prepare the budget, cost allocation plan, financial statements and policies that monitoring reviews.
When does a California nonprofit need an independent audit?
A charity registered with the California Attorney General needs one for any fiscal year with $2 million or more in gross revenue, excluding government grants that already require an accounting. Grant agreements, City contracts and lenders may require an audit at lower revenue, and a Single Audit applies once federal award expenditures reach $1,000,000 in a fiscal year beginning on or after October 1, 2024.
Can RTN CPA do our bookkeeping and our audit?
Not automatically. Professional independence rules restrict the nonaudit services an auditor can provide to an audit client. If we already provide accounting or finance support, we evaluate independence first, and sometimes we recommend another firm for the audit.
Do you work with nonprofits outside San Francisco?
Yes. We work with organizations across the Bay Area and elsewhere in California, and with nonprofits in the other markets listed on this page.
Call (888) 616-8070 or schedule a consultation to get started.
Schedule a Consultation