CentsIQ provides nonprofit bookkeeping services — monthly bookkeeping, fund tracking, grant reporting support, board-ready financials, payroll support, cleanup work, and fractional CFO services. Flat monthly pricing. No guessing. No missed deadlines.

Nonprofit Bookkeeping

Running a nonprofit is not easier than running a business. It is just different.

You still have money coming in, bills to pay, payroll to run, and reports to file. But now you also have donors, grants, fund restrictions, board reporting, public support tests, and Form 990 deadlines to manage.

That is why we offer Nonprofit Bookkeeping. We help nonprofits stay organized, stay compliant, and actually understand their financials without getting buried in spreadsheets.

Key Takeaways

Current nonprofit financial statement language uses net assets with donor restrictions and without donor restrictions
The IRS says Form 990 and 990-EZ are due on the 15th day of the 5th month after year-end
Organizations with gross receipts normally up to $50,000 may file Form 990-N
If unrelated business gross income reaches $1,000 or more, the organization may also need Form 990-T
Missing required filings for three consecutive years can trigger automatic revocation
The federal Single Audit threshold is $1,000,000 for periods beginning on or after October 1, 2024

We Get the Nonprofit World

Nonprofits do not just need clean books. You need a system that supports your mission, your board, your donors, and your reporting requirements.

Tracking of donor-restricted and non-donor-restricted activity
Grant reporting that ties back to the general ledger
Clear audit trails and support files
Budget versus actual reporting by fund, grant, or program
Board-ready financial statements in plain language
Books that support Form 990, Schedule A public support reporting, and year-end tax prep

Many teams still say “restricted” and “unrestricted.” That is normal. But the modern financial statement language is “with donor restrictions” and “without donor restrictions,” and your books should support that correctly.

What Nonprofit Bookkeeping Should Cover in 2026

Requirement	Why it matters
Form 990, 990-EZ, or 990-N filing	The IRS requires annual exempt organization filing, and the 990 series must be e-filed.
Public support tracking	Many 501(c)(3)s need Schedule A to support public charity status.
Unrelated business income review	Nonprofits with enough unrelated business activity may need Form 990-T.
Donor acknowledgments and disclosures	Donors giving $250 or more need proper written acknowledgment support.
Single Audit readiness	If federal awards hit the threshold, your team may need a Single Audit and filing through the Federal Audit Clearinghouse.
Public inspection readiness	Form 990 and 990-EZ are generally subject to public inspection, so the return should match the books.

What We Handle

We take care of the parts that most nonprofit teams find overwhelming:

Monthly bookkeeping and reconciliations
Tracking of donations, grants, pledges, and program income
Fund, class, and grant-level tracking
Budget versus actual reporting for staff and board members
Board-friendly financial statements
Year-end prep for Form 990, Form 990-EZ, or Form 990-N
Support for audits, compliance reviews, and grant reporting
Help with payroll, 1099s, sales tax if applicable, and reporting workflows

We also explain the numbers in plain language, so your board and staff can actually follow what the reports mean.

Stay Ready for Board Meetings, Grant Reports, and 990 Season

Good nonprofit bookkeeping is not just about closing the month. It is about being ready when someone asks a hard question.

Can you show how a public charity used grant funds?
Can you support the numbers that flow into Form 990 or Schedule A?
Can you prove that donor-restricted dollars stayed in the right buckets?
Can you answer a board member’s question without rebuilding the report from scratch?
Can you respond quickly if a grantor or auditor asks for detail?

We build the bookkeeping process so the answer is yes more often, with less scrambling.

Small Teams Welcome

You do not need a full-time finance department to get this right. Many nonprofits operate with a very small staff. Some have one executive director, one operations person, and a board that still needs reliable monthly numbers.

That is exactly where outside bookkeeping support helps. We fill the gap with consistent monthly work, clear reporting, and a process your team can actually maintain.

Tools We Work With

We work with practical tools that nonprofit teams already use, and we help connect them in a way that reduces double entry.

QuickBooks Online with fund tracking
QuickBooks Online for nonprofits
QuickBooks Desktop Enterprise for Nonprofits
Xero for nonprofits
Bloomerang + QuickBooks integration
DonorPerfect + QuickBooks integration
Aplos for teams that want nonprofit-specific fund accounting software
Google Sheets for grant trackers, reconciliations, and support schedules

Already using something else? We can usually work with your current stack. Starting from scratch? We can help set it up with cleaner reporting in mind.

Based in Seattle. Helping Nonprofits Nationwide

We work with nonprofits across Seattle, Portland, Memphis, and beyond. Whether your funding mix is mostly donations, grants, program income, or a combination of all three, we can help you build a cleaner bookkeeping process.

Everything we do is remote-friendly, board-friendly, and audit-friendly.

Frequently Asked Questions

Which Form 990 does a nonprofit file?

It depends on size. The IRS says organizations with gross receipts normally up to $50,000 can usually file Form 990-N. If gross receipts are under $200,000 and total assets are under $500,000, Form 990-EZ may be available. Larger organizations generally file Form 990.

When is Form 990 due?

The IRS says Form 990 and 990-EZ are due on the 15th day of the 5th month after year-end. If you need more time, Form 8868 requests an automatic 6-month extension.

What happens if a nonprofit misses its filings for years?

The IRS says organizations that fail to file required returns or notices for three consecutive years automatically lose tax-exempt status.

Do nonprofits need to send donor receipts?

For donor tax purposes, the IRS says contributions of $250 or more require a written acknowledgment. The IRS also explains substantiation and disclosure requirements for charitable contributions.

When does a nonprofit need a Single Audit?

The federal threshold is now $1,000,000 in federal awards expended for periods beginning on or after October 1, 2024. Audit packages are submitted through the Federal Audit Clearinghouse.

Let’s Take the Stress Out of Your Books

You started your nonprofit to do work that matters, not to chase receipts, rebuild grant spreadsheets, or panic during 990 season.

We help you keep things organized, clear, and ready so you can focus on your mission, your staff, your donors, and your programs.

Flat monthly rates. No guessing. No missed deadlines.

Schedule Your Free Consultation