Bookkeeping Services for Nonprofits | Fund Accounting Experts

Multi-Program & Multi-Grant Operations

For nonprofits running multiple programs, managing several grants simultaneously, or operating across multiple locations, we provide consolidated financial management with program-level segmentation, grant-by-grant budget tracking, and combined organizational reporting. Our team sets up proper class and department tracking so you can evaluate each program’s financial health independently while producing the consolidated statements your board and auditors need. Our financial reporting team produces both program-level and organization-wide financials to give leadership complete visibility.

Budget and Board Reporting

A nonprofit board does not govern from a balance sheet. It governs from the answer to four questions: are we on budget, how fast are we spending the grants, how many months of cash do we have, and what has changed since last meeting. Most bookkeeping stops before those questions get answered, which is why treasurers end up rebuilding the numbers by hand the weekend before a board meeting.

Budget versus actual, every month

Once your budget sits in the accounting system rather than a spreadsheet on someone’s laptop, every monthly close can report actual against budget by line, by program, and by grant. Variances stop being a year-end surprise and become a monthly conversation, while there is still time to act on them.

Grant spending pace

A grant that is 70% through its period with 30% of the funds drawn is a problem, and so is the reverse. We track the burn rate against the award period for each active grant, so the executive director knows which grants need attention before the funder’s report is due.

Cash position and months on hand

Months of operating reserve is the number boards ask about most and the one least often reported. It gets calculated monthly from reconciled figures, alongside a forward cash view that accounts for expected grant receipts and known commitments.

Net assets with and without donor restrictions

Reported separately every month, not reconstructed at year end. When the board asks how much of the cash balance is actually spendable, the answer is already in the statement rather than an estimate from the treasurer.

A board packet that reads like English

Monthly financials are only useful if a board of volunteers can read them. Alongside the statements we can supply a short written note on what moved and why — the lines that shifted against budget, the grants to watch, the cash position — so the finance report takes five minutes of the meeting instead of thirty.

This reporting runs on the same plans as the bookkeeping: $75 a month for 5 hours, with additional hours at $15 an hour, and most organisations with multiple programs, several active grants or a formal board reporting cycle sit on the $300 a month, 20-hour plan. Every plan carries a 100% money-back guarantee on your 1st retainer, refundable on the unused balance.

Form 990 Preparation

We prepare and file the Form 990 series, and we do it from books we have kept all year, which is the part that actually determines what the return costs and how long it takes.

No CPA is required to prepare a 990

This surprises a lot of boards. The Form 990 is an information return, not an income tax return, and nothing in the rules requires a CPA to prepare or sign it. Any paid preparer holding a PTIN may prepare and sign one. What a CPA is genuinely required for is an independent audit or review — which some states mandate above a revenue threshold, and which most large federal grants require. We do not perform audits, and we would not claim otherwise; where your governing documents or a funder require one, we prepare the books your CPA issues the opinion from.

Which return your organisation files

• Form 990-N (the e-Postcard) — for organisations with gross receipts normally $50,000 or less. It is free to file directly with the IRS and takes minutes.
• Form 990-EZ — generally for gross receipts under $200,000 and total assets under $500,000.
• Form 990 — generally for gross receipts of $200,000 or more, or total assets of $500,000 or more.
• Form 990-PF — private foundations, regardless of size.

Thresholds and schedule requirements change, and the right return depends on your organisation’s specific facts. We confirm which applies before any work starts.

What makes a 990 expensive

Almost never the form itself. It is the condition of the records underneath it. A 990 asks for functional expense allocation across program, management and fundraising; revenue separated by source; grants tracked individually; and net assets split by donor restriction. If none of that was maintained during the year, somebody has to reconstruct twelve months of it first, and that reconstruction is the bill.

Organisations whose books we keep monthly arrive at filing season with that structure already in place, because the 990’s categories are the same ones the monthly close uses. Where we are picking up books that are behind, catch-up is published at $75 per month behind, covering up to 5 hours each, with additional hours at $15 an hour from the same retainer — so a full year behind starts at $900, a figure a board can approve rather than a surprise invoice.

Also handled at year end

Form 1099-NEC and 1099-MISC preparation for contractors and vendors, and the supporting schedules your return or your auditor will ask for — functional expense allocation, program revenue breakdowns, grant-by-grant detail, and net assets by restriction.

Software We Support

Nonprofits need accounting platforms that support fund-based tracking, donor management, and grant reporting. Our bookkeepers are proficient in QuickBooks for small-to-mid-size organizations (including its nonprofit chart of accounts templates), Xero for cloud-first nonprofits managing multiple funding sources, and NetSuite for larger organizations needing enterprise-level fund accounting and multi-entity consolidation. We configure each platform to separate restricted funds, track grants, and produce the reports your board and funders require.

We also bring deep expertise to related mission-driven sectors including educational institutions and healthcare organizations, where compliance-heavy financial management and fund-based tracking are equally critical.

Related Resources

Explore these guides for a deeper look at the topics covered on this page:

• Accounting for Non-Profits and Charities

What Our Nonprofit Clients Say

“Great professional, efficient service reasonably priced. Team is always available to respond. Highly recommended.” — Center for Community Inclusion, Inc. — Cockeysville, MD

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