Best Accounting Software for Nonprofits

Jul 22, 2021

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Accounting for a nonprofit organization can feel like spinning plates as you try to manage donations, fundraising, grants and volunteers. The right bookkeeping service can help keep the china from crashing to the ground. And the best nonprofit accounting software helps you spin more efficiently, giving you data and insights along the way.

Here are our top picks for nonprofit accounting software.

Xero: Best for small, growing organizations

Price: Xero offers three plans, billed monthly: Early ($12), Growing ($34) and Established ($65). All new users get a 30-day free trial. Registered nonprofit organizations receive 25% off the monthly fee.


  • Full suite of 100+ reports included with all subscription levels.

  • Syncs with apps like Stripe, PayPal and Infoodle.

  • Easy to use, with online courses to help you get started.


  • No phone support.

Why we like it

Xero is an easy-to-use, easy-to-scale, cloud-based accounting software that can be customized to fit the needs of your nonprofit organization. Need to manage a membership base? Connect Xero with MembershipWorks. Need to track donations? You can link your Xero account to Infoodle for seamless donor communication and analysis.

See NerdWallet’s full review of Xero.

Aplos: Best for accounting and CRM

Price: Aplos starts at $59 per month with the option to add on text-to-give ($20 per month) or advanced accounting ($159 per month). Aplos offers a 15-day free trial and 50% off the first six months if you sign up during that trial. Additional discounts are available for small/new organizations and those that opt for an annual subscription.


  • Designed for nonprofits and churches.

  • Tools to build and host your website.

  • Accept tithes and donations from your website.

  • Online event registration and attendee tracking.

  • True fund accounting with balance sheets and income statements by fund.


  • Accounting features like tax reporting and budget by fund require an upgrade.

Why we like it

Aplos does more than accounting — way more. The cloud-based software is a full-fledged customer relation management tool that allows your organization to easily track, manage and engage members and donors. True Fund accounting features help you stay on top of donation restrictions to ensure funds are spent on time and in the correct manner. And event management tools let you register, track and check in attendees.

The “Advanced Accounting” package is a pricey add-on at $159 per month but unlocks the ability to budget by fund or tag, track fixed assets and automatically complete your annual IRS Form 990.

QuickBooks Enterprise for nonprofits: Best for large organizations

Price: Annual subscriptions range from $1,655 (Gold) to $4,020 (Diamond) for one user. You can add up to 30 or 40 users, depending on the plan. While QuickBooks Enterprise doesn’t offer a discount for nonprofits, as of this writing new users can receive 10% to 40% off the annual cost for their first year.


  • Industry-specific reports to track donors and manage budgets by program.

  • Capable of handling a robust donor database.

  • Priority customer service.


  • Desktop only. Remote access is an additional charge.

  • Expensive annual subscription.

  • Limited to Windows users.

Why we like it

You can tweak most QuickBooks accounting solutions to work for a nonprofit organization, but who has time for that? QuickBooks Enterprise does much of the work for you with a nonprofit chart of accounts that gives a clear picture of your organization’s assets, expenses and revenue, including from donations and retail sales. At tax time, you can easily transfer your data to the relevant IRS forms. Customizable reports allow you to manage budgets for various programs, view contributions by donor and grant and track top-tier donors.

While QuickBooks Enterprise is stacked with features, it also requires a stack of cash to acquire. Annual subscriptions start at $1,655 for one user and there's no discount for nonprofit organizations.

Additional options for nonprofit accounting software

  • Zoho Books: Free for businesses with less than $50,000 in revenue.

  • QuickBooks Online: Scalable software that you can customize with integrated apps.

  • Sage Intacct: Enterprise software with a customer setup for nonprofits.

  • AccuFund: Fundraising and CRM solution for nonprofits.

How to choose accounting software for your nonprofit

Accounting software should solve problems, not create headaches. So the first step in choosing a nonprofit accounting software is to identify the obstacle(s) blocking your work. Then, look for features that can push those roadblocks aside.

That might be robust CRM functions that let you track, analyze and engage a large donor or membership base. Or maybe you need a way to easily accept online donations, along with some basic accounting functions.

Other features to look for:

  • The ability to budget by fund, project and/or tag.

  • Automated reporting for IRS Form 990.

  • Grant management features to meet time and use restrictions.

Balance the features you need alongside your budget and whether the software checks other boxes, like scalability and ease of use, to choose the best accounting software for your organization.