Nonprofit CPA in San Diego, CA
Audits, grant compliance, accounting and Form 990 support for San Diego nonprofits that answer to funders, boards and regulators, and need their numbers to hold up.
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Nonprofit CPA support for San Diego nonprofits
San Diego nonprofits rarely run on one kind of money. A single organization might hold a county contract, a foundation grant with a restricted purpose, a federal award passed through a state department, and a base of individual donors, each with its own rules about what can be spent, when, and how it has to be reported.
Keeping those streams straight is the core of our work. RTN CPA is a certified public accounting firm that serves nonprofit organizations, government agencies and districts, and small businesses. For San Diego organizations that means grant reports that tie back to the general ledger, restricted funds tracked as restricted, program costs accounted for by program, and records that are ready when an auditor asks for them.
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 Diego organizations from our California offices.
Nonprofit audits for San Diego organizations
Most audits start with a requirement someone else set: a grant agreement, a county or state contract, a lender, a board, or the California Attorney General's audit rule for larger registered charities.
Under California Government Code section 12586(e), a charity registered with the Attorney General that receives $2 million or more in gross revenue in a fiscal year (not counting government grants the charity must already account for to the funder) must have its financial statements audited by an independent CPA and make them available within nine months after year end.
- financial statement audits prepared under nonprofit accounting standards
- Single Audits under the Uniform Guidance (2 CFR 200, Subpart F)
- compliance audits tied to specific grants and contracts
- reviews and compilations when a full audit is not required
- communication of internal control findings to management and the board
First audits usually stall on preparation, not fieldwork. Grant documentation, contribution records, net asset classifications and support for functional expenses all need to be in place before testing starts, and we tell you up front what is missing.
An audit is an independent engagement, and we keep it separate from bookkeeping, accounting and advisory work. If RTN CPA is also helping with your books or filling a finance role, we evaluate the AICPA independence rules before accepting an audit, and in some cases another firm will need to perform it.
Grant reporting & Uniform Guidance
Grant money in San Diego often comes in layers. A federal award can reach a local nonprofit through a state department and then a county contract before anyone on staff reads the original terms, and by then it rarely says "federal" on the label.
That matters because a Single Audit is required once federal award expenditures reach $1,000,000 in a fiscal year beginning on or after October 1, 2024 ($750,000 for earlier fiscal years). Spotting that early, and tracking allowable costs, match and reporting deadlines as the year goes instead of rebuilding them when a report is due, is most of the work.
- identifying federal pass-through funding and award terms
- grant and program tracking inside the general ledger
- allowable-cost, match and budget-to-actual reviews
- Schedule of Expenditures of Federal Awards (SEFA) preparation
- funder and county contract reporting support
Form 990 preparation & nonprofit tax
Form 990 is a public document. Foundations, donors and prospective board members read it, and a return that is filed on time but poorly presented (program expenses lumped together, governance questions answered loosely, Schedule O left thin) makes an organization look weaker than it is.
California adds its own filings. Charities registered with the Attorney General's Registry of Charities and Fundraisers generally file an annual Form RRF-1, and exempt organizations generally file Form 199 or the 199N e-Postcard with the Franchise Tax Board. We prepare the federal return and coordinate the state filings so all of them tell the same story.
- Form 990, 990-EZ and 990-PF
- Schedule A public support testing
- Form 990-T and unrelated business income analysis
- California Form 199 and Attorney General RRF-1 filings
- exemption and ongoing compliance questions
Nonprofit accounting & bookkeeping
Plenty of San Diego nonprofits run with one finance person who handles payables, payroll, grant reports, the board packet and audit requests at the same time. Something slips, and it usually shows up at year end.
We set up and keep the accounting a nonprofit actually needs: fund accounting that keeps donor-restricted money separate, grant expenses coded to the right award and period, program costs allocated on a basis you can explain, and a monthly close that produces statements your board can read.
- monthly bookkeeping, reconciliations and close
- fund accounting and restricted-fund tracking
- grant expense tracking by award and period
- functional expense allocation
- budget-to-actual and board-ready financial reports
- audit preparation schedules
Fractional CFO & advisory
Some organizations have outgrown a part-time bookkeeper but are not ready for a full-time finance director. A fractional CFO or controller fills that gap: someone who owns the budget, the cash forecast and the board's financial questions a few days a month instead of five days a week.
For San Diego nonprofits balancing several funding sources, that usually means multi-year budgeting, cash planning around reimbursement-based contracts, and internal controls sized for a small finance team.
- fractional CFO and controller services
- budgeting and cash flow forecasting
- internal controls review and design
- board and finance committee reporting
- financial policies and process improvement
Where San Diego nonprofits get stuck
Most financial problems build slowly. These are the ones we see most often.
- Restricted gifts and grants tracked in a spreadsheet instead of the accounting system
- Federal pass-through funding nobody flagged until a Single Audit was due
- Grant expenses that are hard to tie to a specific award or period
- One person approving, paying and reconciling
- Board reports that show totals but not budget-to-actual results
- Audit preparation that starts after the auditor's first request list arrives
None of these is dramatic on its own. Together they make reporting slow and audits expensive, because the fixes reach back across the whole year.
How RTN CPA works with you
We start with where your organization actually is: your funding mix, the condition of your records, what funders and regulators require, and the deadlines you are working toward.
Scope is agreed in writing before work begins, so it is clear whether you are engaging us for an audit, a review, ongoing accounting or advisory support. Across the firm, RTN CPA has more than 25 years of experience and has completed more than 100 audits, and the firm serves nonprofit organizations, government agencies and districts, and small businesses.
- a first conversation about your revenue, funding sources and deadlines
- a written engagement letter with a defined scope
- a document request list before work begins
- findings and recommendations explained in plain language
No CPA firm can promise a clean audit opinion. What we can do is show you where you stand before fieldwork begins.
Where to start
If you already know what you need:
Serving nonprofits across San Diego County
We work with nonprofits based in the City of San Diego and throughout San Diego County, from downtown and the coastal communities to North County, East County and the South Bay. RTN CPA also offers its services to nonprofits in these markets:
Talk with a San Diego nonprofit CPA
Whether you have an audit coming up, a grant report that will not reconcile, or a board asking for better numbers, start with a short conversation.
Tell us your annual revenue, your funding sources and what is being asked of you. We will tell you what kind of engagement fits (an audit, a review, accounting support or something else) and what it will take to get there.
Questions San Diego nonprofits ask
Does RTN CPA have an office in San Diego?
No. RTN CPA is a California firm with addresses in Los Angeles and Roseville. We work with San Diego County nonprofits through our secure file upload and scheduled phone or video meetings, and if any part of an engagement needs to happen in person, we discuss it when we set the scope.
When does a California nonprofit need an audit?
It depends on who is asking. Charities registered with the California Attorney General that receive $2 million or more in gross revenue in a fiscal year (excluding government grants that already require an accounting) must have an independent CPA audit. Grant agreements, government contracts, lenders and boards can require one at lower revenue levels, and a Single Audit applies once federal award expenditures reach $1,000,000 in a fiscal year beginning on or after October 1, 2024.
What is the difference between an audit and a review?
An audit gives reasonable assurance that the financial statements are free of material misstatement, and it includes testing of the underlying records. A review is narrower: it relies mainly on inquiry and analytical procedures and gives limited assurance. Some funders accept a review and others require an audit, so check your agreements before choosing.
Can the same firm keep our books and audit them?
Not automatically. CPA independence rules limit the nonaudit services an auditor can provide to an audit client. If we handle your accounting or act in a finance role, we assess independence before accepting an audit, and sometimes we will recommend that another firm perform it.
We are a smaller nonprofit. Is it too early to talk to a CPA?
No. Many organizations start with bookkeeping cleanup, grant tracking or a review, then build toward audit readiness as revenue and funder requirements grow.
Do you handle California filings as well as Form 990?
Yes. Along with Form 990 we prepare California Form 199 and help with the Attorney General's annual RRF-1 registration renewal, so the federal and state filings agree.
Call (888) 616-8070 or schedule a consultation to get started.
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