The right nonprofit accounting software helps you track every dollar, stay compliant, and show your board and funders where the money goes. With so many tools on the market, though, choosing one can feel overwhelming.
This guide covers what to look for and walks you through ten of the best options for organizations like yours.
Before you compare tools, it helps to know which features a nonprofit needs. Business accounting and nonprofit accounting are not the same, and a handful of capabilities should be on your list.
Above all, look for these five things:
Keep in mind that software is only as good as its setup.
Even the strongest platform will hand you messy reports if the funds, accounts, and categories are built wrong from the start, so the tool you choose is only one part of the picture.
Here are ten of the best nonprofit accounting software options, ranging from free tools for small teams to full fund accounting systems for larger organizations.
Wave is a free, cloud-based accounting tool that suits very small or brand-new nonprofits.
You can track income and expenses, send invoices, scan receipts, and pull simple financial reports without paying a cent, which makes it a friendly starting point for volunteer-run organizations with straightforward finances. A paid Pro plan adds bank connections and automatic transaction imports to save time on data entry.
The trade-off is that Wave was built for small businesses, not nonprofits, so it lacks true fund accounting. You can track restricted and unrestricted money using categories, but that workaround gets harder to manage as your funding grows.
Zoho Books is an affordable, easy-to-use platform that works well for nonprofits that want more structure than a free tool offers.
You can categorize funds and expenses, track projects, accept donations in multiple currencies, send donation receipts, and give volunteers role-based access from anywhere. Registered charities also qualify for a discount off the regular price.
Like most business tools, it handles funds through categories rather than true fund accounting, so it fits smaller organizations with fairly simple reporting needs.
Xero is a clean, cloud-based platform for people who are not accountants, which makes it a comfortable fit for lean nonprofit teams. It offers a real-time dashboard, clear reports you can share with your board and donors, bank reconciliation from any device, and payroll through its Gusto integration.
Nonprofits can apply for a discount once their status is confirmed.
QuickBooks Online is a widely used accounting software, which means that most accountants and bookkeepers already know it well.
Its higher tiers, Plus and Advanced, let you track income and expenses by fund or program, manage donors and grants, and produce nonprofit reports like the statement of financial position and budget versus actual. It also organizes your data to make Form 990 prep simpler at year-end.
Because it is so common, QuickBooks connects to a huge range of tools, including nonprofit favorites like DonorPerfect. Fund tracking lives in the pricier plans and takes some careful setup, but overall, QuickBooks fits organizations that want a familiar system their accountant can step right into.
Learn more about QuickBooks for nonprofits.
Aplos is one of the tools on this list specifically for nonprofits and churches, with true fund accounting at its core.
It tracks restricted and unrestricted balances automatically, produces board-ready and audit-ready reports in a click, lets you budget by grant or program, and comes with Form 990 mapping already set up. Aplos also bundles in donor management and online giving as part of its wider Velora suite, so your gifts and your books stay connected.
MonkeyPod is an all-in-one platform for nonprofits, pairing true fund accounting with donor management, grant tracking, online fundraising, and email outreach in a single system. Because everything runs on the same data, a donation flows straight from your fundraising page into your books and updates the donor's record along the way, with no exporting or double entry.
It produces audit-ready financial statements and funder reports in a few clicks, and its plans come with unlimited users, records, and transactions.
MIP is a dedicated fund accounting system with roughly 40 years behind it, built for nonprofits, schools, and government organizations. It tracks unlimited funds through a flexible, multidimensional chart of accounts, and handles grant reporting, budgeting, and FASB-compliant statements.
MIP fits established and larger organizations that juggle multiple funding sources and strict reporting requirements.
Sage Intacct is a cloud financial platform aimed at midsize and growing nonprofits, and it offers true fund accounting.
It comes with a dimensional general ledger, grant tracking and billing, revenue recognition, and push-button consolidations across multiple entities, all backed by strong real-time dashboards and reporting. Built-in AI tools flag errors and automate routine work like bill entry and reconciliation.
Financial Edge NXT is purpose-built fund accounting from Blackbaud, the largest name in nonprofit technology. It uses a segmented chart of accounts and subfund tracking to handle grants, endowments, and restricted funds in fine detail, with strong compliance controls, role-based access, customizable dashboards, and AI-assisted reconciliation.
Financial Edge NXT fits established and larger organizations.
NetSuite is a full cloud ERP from Oracle, with nonprofit accounting as one part of a much larger system. It connects fund, grant, donor, and program data in one place, letting you tag every transaction by fund, program, grant, or donor restriction while supporting FASB standards and Form 990.
NetSuite fits large, complex nonprofits, often those working across multiple entities or countries, that need far more than accounting alone.
Every platform on this list can track your funds and produce clean reports, but none of them can tell you whether your funds are set up correctly in the first place.
Software records what you put into it, so if the chart of accounts is wrong, the funds are misclassified, or a grant is tracked in the wrong place, you get polished reports with bad numbers.
Someone still has to configure the system around how your organization is funded and keep the books accurate month after month. A good bookkeeper, accountant, or CPA does that work, and the software simply gives them a better place to do it.
QuickBooks is the most common choice, especially for small and midsize nonprofits, because it is affordable, widely supported, and familiar to most accountants. As organizations grow and their funding gets more complex, some move to purpose-built fund accounting systems like Aplos, MIP, Sage Intacct, or Blackbaud Financial Edge NXT.
QuickBooks Online plans currently range from around $38 per month for the basic tier up to about $340 per month for the top tier, but promotional discounts are common. For nonprofits, fund and program tracking lives in the Plus and Advanced plans. Many organizations get discounted or donated access through TechSoup, a marketplace that offers reduced pricing on software for eligible nonprofits.
Most established nonprofits use the accrual method, which records income when it is earned and expenses when they are incurred, rather than when cash actually changes hands. Accrual accounting is required under GAAP and is what auditors and most funders expect to see, so it becomes the standard as an organization grows.
Very small nonprofits sometimes start on the cash method because it is simpler, and then switch to accrual as their finances and reporting needs expand.
There is no separate nonprofit version of QuickBooks Online, but the software can be set up to work for nonprofits. On the Plus and Advanced plans, you can use classes, locations, and program tracking to handle funds and produce nonprofit-style reports like the statement of financial position.
The right accounting software is important, but it only works when it is set up correctly, and someone keeps the numbers clean and meaningful. Your software can't do that on its own.
Complete Balance Accounting & Consulting is an experienced CPA serving nonprofits in the Philadelphia and Cherry Hill, NJ area, offering bookkeeping, controller, and outsourced accounting services.
If your nonprofit is ready to turn its accounting software into financial clarity, reach out and let's set your organization up for long-term success.
