Bookkeeping, payroll, and CFO services for San Diego's small businesses.

Call or Text: (619) 417-8735

Nonprofits

Fund accounting that tracks donor intent and grant requirements. We prepare your books for 990 filing and keep your board informed.

The Industry

Nonprofit accounting is different at its core. You’re not tracking profit margins or owner distributions. You’re tracking how donor and grantor funds are being used. Every dollar that comes in carries expectations. Some money can be spent however the organization needs. Other funds are restricted to specific programs, time periods, or purposes. The accounting has to reflect this reality or the books become meaningless.

San Diego County has thousands of registered nonprofits ranging from small community groups to established churches to animal welfare organizations. Most operate with lean staff and tight budgets. The person running programs is often the same person managing the books. When the mission takes priority, and it should, the financial tracking falls behind. But funders, boards, and regulators still expect accurate reports. The IRS still wants a Form 990. Grant foundations still want expense documentation.

Who This Covers

Churches and religious organizations. Animal shelters and rescue groups. Youth programs and educational nonprofits. Arts and cultural organizations. Community foundations and service organizations. Any tax-exempt organization in San Diego County managing donor funds, grant money, or program budgets.

What Makes It Different

Fund accounting requires tracking money by source and restriction. Grant compliance means documenting every dollar spent on funded programs. Form 990 requires organized records and specific disclosures. Board members need reports they can actually interpret. Donors expect their gifts to be used as intended and want acknowledgment for their tax records.

What We Handle

We set up and maintain proper fund accounting in QuickBooks Online. This means separating restricted funds from unrestricted operating money. When a donor gives to a specific program, that money gets tracked separately from general operating funds. When a grant requires expense reporting, we categorize costs so the reporting process is straightforward. You can see at any time what funds are available for general use and what money is committed to specific purposes.

We prepare the financial reports your board needs to fulfill their oversight responsibilities. This isn’t a dump of accounting data. It’s a clear presentation of where money came from, where it went, and what’s left. When 990 season arrives, we work with your CPA to provide organized records. For organizations with grant funding, we track expenses against budgets so grant reports are accurate when the funder asks for them.

Fund Accounting and Tracking

Restricted and unrestricted fund separation. Program expense tracking tied to specific funding sources. Grant budget to actual reporting. Clear visibility into available funds by purpose. Monthly reconciliation and financial close so you always know where things stand.

Reporting and Compliance

Board-ready financial statements each month in a format that makes sense for nonprofits. Budget vs actual reporting for programs. 990 preparation support with organized records for your tax preparer. Grant expense documentation pulled directly from properly categorized books.

What Goes Wrong

The most common problem is restricted fund confusion. A foundation gives $20,000 for a youth program. That money sits in the same bank account as everything else. Six months later, the general operating account is low and nobody remembers which dollars belong where. The grant money gets spent on rent and utilities. When the program report is due, there’s nothing left to spend on the actual program. This creates real problems with funders and can jeopardize future grants.

Board members often receive financial reports they don’t understand. A standard profit and loss statement doesn’t make sense for a nonprofit because there isn’t supposed to be profit. Without proper fund accounting presentation, board members can’t fulfill their fiduciary duty. They’re approving budgets and signing off on reports they can’t interpret. This is uncomfortable for everyone and creates risk for the organization if something goes wrong.

Grant and Donor Problems

Restricted funds spent on unrestricted purposes without anyone realizing it. Grant expenses not tracked against program budgets. Reports to funders that require reconstructing months of transactions. Documentation gaps that turn audit or review engagements into painful excavations of old records.

Internal Confusion

Volunteer treasurers who know personal finance but not nonprofit fund accounting. Staff turnover that means nobody knows where things were filed or why accounts were set up a certain way. Executive directors spending their evenings on bookkeeping instead of programs or development. Board members voting on financials they don’t fully understand.

What Changes

Fund tracking becomes clear. You can pull a report any time and see unrestricted funds available for operations, restricted funds sorted by program or purpose, and exactly where grant money has been spent against budget. When a board member asks about a specific fund, the answer is immediate. When a grant report is due, the numbers are already organized. No more reconstructing the year to figure out what got spent where.

Your board receives financial reports designed for nonprofit governance. They show sources of funds, program expenses, and administrative costs in a format that makes sense for a mission-driven organization. Your executive director or program staff can focus on the actual work you’re there to do. When it’s time to file the 990, your CPA or tax preparer gets organized records instead of a folder of bank statements and questions.

Fund Clarity

Restricted funds tracked separately from day one. Grant budgets compared against actual spending as the year progresses. Clear reports showing available funds by restriction. No more guessing which money can be spent on what or scrambling when a funder asks for documentation.

Governance and Compliance

Monthly financials the board can actually use to make decisions. 990 preparation that doesn’t require a year-end scramble. Grant reports pulled directly from properly categorized books. Clean records ready if you ever need an audit or review engagement.

San Diego's Small Business Bookkeeper

The Next Step:
A Short Conversation

A quick call to tell us about your business. We'll listen, answer your questions, and give you a clear price quote.

Fresh Ledger provides full-service bookkeeping for San Diego County's small businesses. We handle monthly financials, payroll setup, and part-time CFO services for local business owners who want their numbers done right.

Client Reviews

5-Star Rated Firm
  • Intuit ProAdvisor Platinum Tier badge
  • QuickBooks Online Certification Level 1 badge
  • QuickBooks Online Payroll Certification badge

© 2026 Fresh Ledger LLC