Nonprofit Accounting & Compliance

Nonprofit Accounting & Compliance Services

Nonprofit accounting has rules that most general practice firms get wrong. Our team specializes in fund accounting, Form 990 preparation, grant compliance, and board-ready financial reporting. We help tax-exempt organizations keep clear records, report to funders, and focus on their mission instead of spreadsheets.

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Free initial consultation · No obligation

Best for nonprofits with grants, restricted funds or an audit ahead
Licensed CPA firm
Fees quoted upfront, in writing

Who handles accounting and Form 990s for nonprofits?

Your Virtual CPA is a licensed CPA firm that handles nonprofit bookkeeping, fund accounting, grant tracking, board reports and Form 990 preparation. We help organizations prepare for their audit and keep restricted funds clear. Request a free consultation to talk through your organization.

What's Included

Form 990, 990-EZ, and 990-PF preparation

Fund accounting setup and management

Grant tracking and compliance reporting

Restricted vs. unrestricted fund classification

Functional expense allocation

Board financial reporting packages

State charitable registration filings

Tax-exempt status application (Form 1023/1024)

Unrelated Business Income Tax (UBIT) analysis

Donor acknowledgment letter templates

Audit preparation and support

Budget-to-actual reporting by program and grant

Who This Is For

501(c)(3) Organizations

You run a charitable nonprofit and need a CPA firm that understands fund accounting, Form 990 nuances, and how to keep your financial reporting aligned with donor and funder expectations.

Grant-Funded Programs

You receive federal, state, or foundation grants and need accurate tracking of expenditures by grant, proper cost allocation, and timely compliance reports to maintain funding.

New Nonprofits Seeking Tax-Exempt Status

You are forming a new nonprofit and need help structuring your organization, applying for 501(c)(3) status with the IRS, and setting up proper accounting from day one.

Nonprofits Preparing for an Audit

Your funder or board requires audited financial statements and you need help getting your books audit-ready, selecting an engagement format, and passing with clean findings.

Our Process

Nonprofit Financial Assessment

We review your current accounting setup, chart of accounts, fund structure, and compliance obligations. You receive a clear action plan identifying gaps and priorities.

Fund Accounting Setup

We configure your accounting system to properly track restricted, temporarily restricted, and unrestricted funds. We establish grant tracking codes, functional expense categories, and program-level reporting.

Ongoing Accounting & Reporting

Each month we reconcile accounts, classify transactions by fund and program, and deliver board-ready financial reports including a statement of activities, statement of financial position, and functional expense statement.

Annual Compliance & Filing

We prepare and file your Form 990, state charitable registrations, and any required grant compliance reports. We coordinate directly with your auditors if an audit is required.

Why Choose Your Virtual CPA

Deep specialization in nonprofit accounting and compliance

Experience with single audits, OMB Uniform Guidance, and Yellow Book standards

Board-ready financial packages delivered monthly

Expertise across 501(c)(3), 501(c)(4), 501(c)(6), and other exempt organizations

Proactive grant compliance monitoring to prevent funding clawbacks

Form 990 preparation that tells your story accurately to donors and regulators

Frequently Asked Questions

Form 990 is due on the 15th day of the 5th month after the end of your fiscal year. For calendar-year organizations, that is May 15. You can file Form 8868 for an automatic six-month extension, pushing the deadline to November 15. However, even with an extension, we recommend filing as early as possible since the 990 is a public document that donors, grantors, and watchdog organizations review.

Fund accounting is an accounting method that tracks resources by their intended purpose rather than combining everything into one general ledger. For nonprofits, this means separating restricted grants, board-designated funds, and unrestricted operating dollars so you can demonstrate to funders that their money was spent as intended. Without proper fund accounting, you risk grant compliance issues, inaccurate financial statements, and potential loss of funding.

Start at least three to six months before your fiscal year-end. Ensure all bank accounts are reconciled monthly, grant expenditures are tracked with proper documentation, functional expense allocations are supported by reasonable methodology, and board minutes reflect key financial approvals. We offer an audit readiness review that identifies issues before your auditors arrive, which significantly reduces fieldwork time and the likelihood of audit findings.

Yes. We prepare and file Form 1023 or Form 1023-EZ with the IRS on your behalf. This includes drafting the required narrative descriptions, financial projections, and supporting schedules. We also advise on governance best practices, conflict of interest policies, and initial accounting setup so your organization is built on a solid foundation from the start.

Related Services

Audit, Review & Compilation

Single audits, Yellow Book audits, and financial statement reviews for nonprofits that require independent assurance.

Bookkeeping & Accounting

Monthly fund accounting, reconciliation, and financial statement preparation for nonprofit organizations.

Virtual CFO Services

Strategic financial guidance for nonprofit executives, including budgeting, forecasting, and board financial reporting.

Serving clients nationwide

Virtual CPA services for clients anywhere in the U.S. Local tax guides:

Washington DC Maryland Virginia

Ready to talk it through?

Schedule a short call to discuss your nonprofit accounting & compliance needs.