The 8 Best Accounting Software for Nonprofits in 2021

The best accounting software for nonprofits should offer nonprofit-specific features like fund-based accounting, donation tracking, and Form 990 generation. Looking for software that meets that criteria? Check out's 10 picks for this year's best nonprofit accounting software solutions.
Best overall
Sage Intacct
  • Icon Pros  Dark
    Comprehensive nonprofit and accounting features
  • Icon Pros  Dark
    Stand-out customer service
Best nonprofit-specific
aplos logo
  • Icon Pros  Dark
    Built specifically for nonprofits and churches
  • Icon Pros  Dark
    Built-in website hosting
Best automation
Zoho Books
  • Icon Pros  Dark
    Affordable starting price ($9/mo.)
  • Icon Pros  Dark
    Customizable task automation
Most scalable
Nonprofit Plus
  • Icon Pros  Dark
    Fund-based and encumbrance accounting
  • Icon Pros  Dark
    Inventory management
Best for collaboration
  • Icon Pros  Dark
    Unlimited users for easy task delegation
  • Icon Pros  Dark
    25% discount for registered nonprofits

Nonprofit organizers need a fast, secure way to track finances, accept donations, and draw up reports. In a word (well, two), they need accounting software. While traditional small-business software companies like Sage offer nonprofit discounts and features, nonprofit-specific software like Aplos were tailored to nonprofits' needs right from the start. So which type of software is right for your needs?

If you're trying to decide on a cloud-based nonprofit software service, has your back. Below, we review our favorite nonprofit accounting software options for 2020, from Sage Intacct to QuickBooks and beyond.

Our methodology

To rank the best accounting software for nonprofits, we first considered whether the software offered nonprofit-specific features, like donation tracking and Form 990 generation. We also considered price, ease of use, data security, types of plans, and customer reviews.

The best accounting software for nonprofits in 2020

Best nonprofit accounting software 2020

Brand name
Starting price
Free trial
Nonprofit features
Learn more

Sage Intacct

Contact for quote30 daysFund accounting, Form 990, donation tracking, grant management


$59.00/mo.15 daysFundraising tools, website hosting, church accounting

Zoho Books

$9.00/mo.14 daysMulti-currency acceptance, thorough reporting


Contact for quoteNoneInventory management, time tracking, board management


$9.00/mo.30 daysUnlimited users, third-party app integration

Data effective 9/5/20. At publishing time, pricing and features are current but are subject to change. Offers may not be available in all areas.

Sage Intacct: Best overall


Want the most comprehensive nonprofit accounting software around? Sage Intacct is hard to beat, though its comparatively higher price makes it a better fit for bigger, established nonprofits.

Sage Intacct sets a high standard for what nonprofit organizers should expect from their software. Along with typical accounting features like bank reconciliation, the software supplies a host of tools geared specifically towards nonprofits:

  • Straightforward donation tracking
  • Fundraising, membership, and dues management
  • Form 990 generation
  • Fund accounting
  • Thorough financial reporting

Sage Intacct also offers free seminars to help nonprofit organizers get off the ground—which is particularly useful for nonprofits struggling to make ends meet during the COVID-19 era. And according to customers on the review site TrustRadius, where the company scores 8.5 stars out of 10, Sage Intacct's customer service team is super responsive.1

Here's the problem: Sage Intacct is expensive. Users report prices starting at $8,000 a year and climbing as high as $15,000 (or more). Unfortunately, you have to contact the company directly for a quote—while Sage Intacct claims its customers enjoy a 250% return on investment, there isn't any transparent pricing on the site.2

Pro Bullet Comprehensive nonprofit features, including fund-based accounting
Pro Bullet Time-saving automation
Pro Bullet Free nonprofit seminars
Con Bullet High starting price
Con Bullet No transparent pricing on site

Aplos: Best nonprofit-specific

aplos logo

While Aplos doesn't have as many accounting features as competitors like Sage Intacct, its high-quality, nonprofit-specific features and add-ons help it stand out above the crowd.

Aplos has been nonprofit and church-specific since day one. It's grounded in fund-based accounting, so you don't need to customize your software's built-in general ledger for nonprofit-specific accounting needs. Aplos Suite, which starts at $59 a month, includes a full range of features that work for nonprofit and church accounting alike:

  • Donor relationship management
  • Member and volunteer portals for easy online management
  • Aplos-hosted, easily customizable websites
  • Event registration
  • Automated donation receipts, thank-you emails, and donation reminders
  • Fundraising campaign management

A slew of discounts help make Aplos' software more accessible to smaller nonprofits. New-user promos drop your cost to just a dollar a month for the first three months. Paying annually saves you 10%. And if your nonprofit is less than a year old or makes less than $50K annually, you might qualify for additional discounts.

While Aplos excels at the nonprofit portion of nonprofit accounting software, its accounting focus leaves a little to be desired. You'll have to pay extra for accounting software standards like end-of-year tax form generation, expense tracking, and comprehensive financial statements.

Pro Bullet Nonprofit-specific software
Pro Bullet Built-in website hosting
Pro Bullet Church management features, including online tithing acceptance
Con Bullet No built-in bookkeeping (add-on only)
Con Bullet Pricey accounting plan ($159 per month)

Zoho Books: Best automation

Zoho Books

Zoho Books saves you time by automating as many accounting tasks as possible. With its affordable plans, fully functional app, and easy collaboration, Zoho works nicely for small, on-the-go nonprofits.

Zoho Books is one of our favorite online accounting software options, and it has plenty of features that transfer nicely to nonprofits' needs. For one, it's affordable: plans start at $9 a month (or $7.65 with a 15% discount for nonprofit). Like Sage, Zoho includes thorough reporting, including expense reports that simplify transparency and fund tracking. And Zoho excels at collaboration—you can delegate as many tasks as you need to other organization members.

Zoho also offers thorough automation in the form of workflows, which are customizable, automated tasks and alerts you can set up to streamline company processes. For instance, a particularly high donation can trigger an automatically emailed thank-you note and tax receipt. (You can learn more about workflows on our Zoho Books review.)

But if you want to accept donations—which you undoubtedly do—you can't just sign up for Zoho Books. You also need Zoho Checkout, Zoho's payment portal. Zoho Checkout is free as long as you accept only 50 donations—ever, not per month. Clients that need unlimited donations in multiple currencies will need to add a $9-a-month Zoho Checkout plan to their existing Zoho Books plan.

And we can't in good conscience recommend Zoho Books to anyone who pays more than one or two employees. Zoho doesn't offer its own payroll solution, and it doesn't integrate with third-party payroll software either.

Pro Bullet Task automation
Pro Bullet Unlimited users
Pro Bullet Multi-currency donation acceptance
Con Bullet Not built specifically for nonprofits
Con Bullet No easy payroll integration

NonProfitPlus: Most scalable


NonProfitPlus' thorough range of features blend the best of the nonprofit and accounting worlds—though at a relatively steep price.

Aplos wins big for nonprofit features, and Zoho Books wins big for accounting, but NonProfitPlus gives you the best of both types of software. Its nonprofit accounting package includes donor management, board management, and unlimited users for easier delegation. Its financial management suite includes fund-based and encumbrance accounting, which makes for easier budget tracking.

You can even manage and track time and expenses to make sure you're making the most of your resources. And with so many features, NonProfitPlus is super scalable: as your organization grows, more NonProfitPlus features (for instance, delegation and time tracking) become relevant. Most importantly, unlike most nonprofit software, NonProfitPlus includes inventory management, which is crucial if you sell merch to raise money or reward donors.

On the flip side, NonProfitPlus doesn't list any pricing on its site—as with Sage Intacct, you have to get in touch with a representative for a quote. Customers report paying more than $600 a month for NonProfitPlus' full suite of features, so if you're looking for affordable nonprofit software, NonProfitPlus probably isn't it.

Pro Bullet Unlimited users
Pro Bullet Inventory management
Pro Bullet Thorough accounting and nonprofit features
Con Bullet More expensive than most competitors
Con Bullet No clear pricing on site

Xero: Best for collaboration


Want to share financial oversight with other members of your organization? Unlike most accounting software, Xero lets you add as many users as you want for no additional charge.

Xero is our absolute favorite small-business accounting software, and its strengths transfer remarkably well to nonprofit accounting. For starters, Xero surpasses nearly every other cloud-based accounting software solution in one key area: collaboration. While QuickBooks limits your user number by plan and FreshBooks charges an extra $10 per user per month, Xero includes unlimited users.

Of course, NonProfitPlus and Zoho Books also offer unlimited users—but Xero's pricing easily beats out NonProfitPlus'. Plus, Xero integrates with hundreds more apps than Zoho Books, which mostly integrates with other Zoho apps.

Xero also excels at accounting basics that can keep your nonprofit's budget on track, like financial reporting and expense tracking. And its highly rated mobile accounting app means your organization can collaborate on the go.

But since Xero wasn't built for nonprofits, it doesn't include the same targeted features as, say, Aplos. Most importantly, it doesn't offer true fund-based accounting. If you want collaboration and fund-based accounting (and don't care as much about price), NonProfitPlus is a better pick.

Pro Bullet Unlimited users
Pro Bullet Affordable plans starting at $9/mo.
Pro Bullet Excellent mobile app
Con Bullet No true fund accounting
Con Bullet Fewer nonprofit-specific features than competitors

Tailored recommendation for your business

Nonprofit accounting software runner-ups

Didn't find your software match above? Not to worry—there's more where those came from. See if one of these five additional nonprofit software solutions fit your needs.

Oracle NetSuite: Most comprehensive

NetSuite, which was purchased by Oracle a few years ago, offers a wide range of accounting and ERP (enterprise resource planning) solutions for dozens of industries—including nonprofits. NetSuite's cloud-based Social Impact software includes fund accounting, inventory management, and even ecommerce support.

Unfortunately, NetSuite's site is pretty sparse. We think most nonprofits are eligible for a completely free version of NetSuite Social Impact . . . but the site is confusing enough that we can't say for sure. For small businesses, Oracle Netsuite runs at about $99 per user per month on top of a pricey base fee. Hopefully, NetSuite's discount for nonprofits knocks your cost down quite a bit, but the total price might be more comparable to Sage Intacct than Xero or Zoho Books.

Wave: Most affordable

Wave's accounting software is completely free for nonprofits and small businesses alike. And for free software, it sure packs a punch: along with a general ledger, you'll get thorough financial reporting, income and expense tracking, and multi-currency payment acceptance.

Wave also offers a complete suite of (mostly free) products to round out your nonprofit accounting experience. For instance, Wave Payments lets you process donations, and the transactions immediately sync with your Wave Accounting software. Wave also offers its own payroll solution that starts at just $20 a month—and once you start shopping around for payroll software, you'll see what a steal Wave Payroll can be.

But like a lot of providers on our list, Wave wasn't built for nonprofits, so fund accounting is a no-go. And since it offers just one free plan, Wave's software isn't particularly scalable. It works best for small nonprofits that plan to stay small, not for organizations that hope to grow.

Best Bookkeeping Software
Best for freelancers
Best for global ventures
Best for midsize
Best for invoicing
Learn more about our top brands.

QuickBooks Online: Most user-friendly

By any measure, QuickBooks Online, Intuit's cloud-based accounting software, is absolutely stellar. With a low learning curve and accessible dashboard, it's a good pick for beginners who lack a strong accounting background . . . but only those who are willing to pay a steep $25 a month.

QuickBooks does offer nonprofit-specific desktop software that includes some donation tracking features. But honestly, the QuickBooks desktop version isn't as flexible as the cloud-based version. And QuickBooks itself recommends simply customizing your QuickBooks Online plan instead of choosing desktop software.

NonProfit Treasurer: Best free alternative

NonProfit Treasurer was built for (you guessed it) nonprofit treasurers, particularly volunteer treasurers. The software uses automatic bank syncing and expense tracking to streamline nonprofit budgeting. And while its nonprofit financial reports aren't the most detailed, NonProfit Treasurer's reporting templates are easy to generate, download, and share with stakeholders.

But NonProfit Treasurer's site is the least fleshed-out of all our options, and while its user reviews are high, those numbers come from only a handful of people. The bare-bones site and low user numbers aren't enough for us to scratch NonProfit Treasurer off our list, but we do recommend you do a little more digging before signing up.


Not all accounting software builds budgeting into the package, but MoneyMinder is different. With easy budgeting and forecasting, you can plan for future donations and ensure your organization is on track to spend every cent where it can do the most good.

However, while MoneyMinder has accounting basics like accounts receivable and payable, it doesn't have a general ledger, which makes tracking those accounts a little trickier. It doesn't operate around fund-based accounting either. Since larger organizations need both a GL and fund accounting, we recommend MoneyMinder's nonprofit accounting solution to small nonprofits, HOAs, or church groups only.

Find Your Money—and Keep More of It

With plans starting at $15 a month, FreshBooks is well-suited for freelancers, solopreneurs, and small-business owners alike.

  • Track time and expenses
  • Create custom invoices
  • Accept online payments

Nonprofit accounting software FAQ

Is there a QuickBooks plan for nonprofits?

Yes. QuickBooks offers a nonprofit-specific desktop plan called Desktop Premier Nonprofit. The software starts at $499.95 per year (or $299.95 for the first year based on the current promotion) and includes a few useful nonprofit tools:

  • End-of-year donation statements
  • Donor contribution summary reports
    Form 990 generation

Still, even QuickBooks recommends that nonprofits try their cloud-based software, QuickBooks Online, instead. QuickBooks Online, while expensive, is cheaper than the desktop software with more flexibility and functionality.

Which accounting software is best for nonprofits?

In our opinion, Sage Intacct is the best accounting software for nonprofits: it has the most comprehensive features and integrates easily with many third-party apps.

But the best nonprofit accounting software for you might be different. For instance, Sage is a lot more expensive than options like Zoho Books, which makes it better suited to large, long-established organizations. Meanwhile, Zoho's free plan with its nonprofit integration is perfect for small, just-launched nonprofits.

So how can you pick the perfect software for you? Make sure to weigh your organization's unique needs against the software's features and pricing. And take advantage of those free trials—it's perfectly fine to shop around before settling on one plan.

What is fund accounting?

Fund accounting, also known as fund-based accounting, is the accounting system nonprofits use to keep their books and track funds.

Typical small-business accounting revolves around profit—how much a company is making, spending, losing, and saving. In contrast, nonprofit accounting centers on tracking funds, including responsible oversight of fund management. Fund accounting software's primary goal is to show you and your shareholders, namely board members and donors, exactly where their money is going.

What is Form 990?

Form 990 is a tax form that tax-exempt organizations—which includes most nonprofits—must submit to the Internal Revenue Service (IRS) every year. The form details your organization and aims and shows where your funds came from and were distributed during the tax year. Unlike individual and small-business end-of-year tax forms, Form 990 is available for the public to view.

Does nonprofit accounting software include payroll?

As with typical accounting software, most nonprofit accounting software doesn't include payroll. If you're paying employees, you'll have to purchase a separate payroll plan, preferably one that syncs with your accounting software to simplify data entry and financial tracking.

You can find a handful of free payroll software options, but frankly, we don't recommend them for nonprofits (or even for most small businesses). Instead, we recommend checking out pricier-but-less-risky options like Gusto and Wave Payroll that should do right by your employees.

What happened to Blackbaud?

Blackbaud frequently makes top 10 lists for the best accounting software for nonprofits. However, in July of 2020, Blackbaud reported that it had been hacked much earlier in the year. The resulting data breach impacted over 120 nonprofits in the UK alone.3

Blackbaud's data breach isn't necessarily unusual—cyberattacks are, unfortunately, par for the course for online businesses and organizations. But the fact that Blackbaud experienced the breach in February, noticed it in May, and didn't tell clients about it until July had a lot of customers on edge.3 Due to both the breach and the failure to immediately notify clients, we've left Blackbaud out of our top 10 for now.

We'll keep monitoring the situation and see if Blackbaud earns its way back into our rankings.

The takeaway

Finding a software that really clicks with you is integral to your success, so make sure to snag those free trials and test-drive different options. After all, with the right bookkeeping software on your side, you'll be able to make the most of your donations and reach people who support your cause.

Need to save money while you get your new nonprofit off the ground? Our list of the year's best free accounting software can help you keep your books in order while you plan for growth.


At, our research is meant to offer general product and service recommendations. We don't guarantee that our suggestions will work best for each individual or business, so consider your unique needs when choosing products and services.

1. TrustRadius, "Sage Intacct Reviews." Accessed September 4, 2020.
2. Sage Intacct, "Pricing," 2020. Accessed September 1, 2020.
3. Paul Clolery, The Nonprofit Times, "The Hack of Blackbaud: Damage is Still Being Assessed," August 6, 2020. Accessed September 4, 2020.

Kylie McQuarrie
Written by
Kylie McQuarrie
Kylie is an accounting writer for Kylie spent two of the last four years writing for and with small-business owners—from dentists in Australia to plumbers in the Midwest. She spent the other two writing in depth about internet and security. She’s passionate about reading, hiking, and dedicating every spare second to writing for fun (at lunch, between meetings, on the train, before breakfast . . . ). Her content helps small-business owners tackle the logistics of running a business so they can focus more on their passions too.
Recent Articles
The Best Bookkeeping Software for Small Business 2021
To find the best bookkeeping software for small-business owners, we looked at key bookkeeping features...
Wave vs. QuickBooks Online: Which Accounting Software Is Best for Small Businesses?
We compared Wave’s and QuickBooks’s accounting features, pricing, plans, customer reviews, and ease of use...
Best Billing and Invoicing Software for Small Businesses 2021
We weighed top invoicing softwares’ payment options, customization, and pricing—plus customer service reputation and ease...
A black male waiter serves a group of black and white women eating at a restaurant
Best Payroll Software for Restaurants 2021
Restaurant owners have unique payroll needs, like meeting minimum wage requirements while factoring in tips....