Aplos vs Quickbooks: Uncovering which accounting software is right for you

Finding the right accounting software isn't just a tech decision. It's a mission-critical investment. Nonprofits face unique challenges when it comes to managing finances: fund accounting requirements that for-profit systems don't address, grant management complexities, and stakeholder reports that need to tell your financial story with accuracy and transparency. When you choose software designed specifically for nonprofit needs, you're not just checking a compliance box—you're able to work smarter, demonstrate outstanding stewardship, and ultimately create more bandwidth to focus on what really matters: the communities you serve.

The right accounting solution doesn't just organize your numbers—it amplifies your impact. If you're trying to decide between Aplos or QuickBooks for your nonprofit accounting needs, this guide will help you make an in-depth comparison. Let's get started!

What is Aplos?

Aplos takes the complexity out of nonprofit finances, giving you a straightforward system that understands the unique way nonprofits and faith-based organizations need to track and report their money.

What makes Aplos shine is its laser focus on true fund accounting principles. You'll track every dollar across multiple funds with ease, create board-ready financial reports in seconds, and maintain the rock-solid compliance your organization needs. It's like having a CFO and tech guru that speaks nonprofit fluently—delivering the professional-grade accounting you need without requiring a PhD to use them.

What is QuickBooks?

QuickBooks is the Swiss Army knife of business accounting software that is designed to help businesses of all sizes track income and expenses, process payroll, manage invoices, and handle tax preparation. It offers cloud-based and desktop options with tiers that scale with your business.

QuickBooks excels at general business accounting, but it wasn't built specifically for nonprofits or fund accounting. While QuickBooks can be customized for nonprofit use, you'll need workarounds and add-ons to achieve what Aplos delivers natively.

Feature Comparison: Fund Accounting

Native fund accounting capabilities in a purpose-built system can significantly reduce accounting complexity while strengthening your ability to operate with financial transparency. Here's how Aplos and QuickBooks compare when it comes to fund accounting functionality:

Feature Comparison: Budgeting

Strategic budgeting helps nonprofit leaders balance funding restrictions with organizational priorities, ensuring every dollar advances your mission while maintaining transparency. Here's how Aplos and QuickBooks compare when it comes to budgeting functionality:

Feature Comparison: Reporting

Nonprofit-specific reporting ensures compliance, accurately tracks restricted funds, and generates the specialized reports needed for board governance and donor transparency. Here's how Aplos and QuickBooks compare when it comes to reporting functionality:

Why do nonprofits prefer Aplos to QuickBooks?

Every year, thousands of nonprofits make the switch from QuickBooks to Aplos to access critical fund accounting tools that nonprofits depend on for accurate financial tracking and reporting. Here’s what Aplos customers have said:

• “We switched from Quickbooks to Aplos nearly three years ago, and we’ve never regretted the switch for one second. Using software designed specifically for a nonprofit makes a world of difference.” (Kevin L.)
• “Aplos is much more nonprofit friendly than QuickBooks. It is tailored specifically for nonprofits and is especially helpful for those with bookkeepers who aren't full-time.” (Susanne E.)
• “I used QuickBooks and hated it. [Aplos] is so much easier to do accounting. Very straightforward, easy to see at a glance, and know what is going on. Reports are easy to come by and if you cannot figure something out support is easy to get.” (Pamela K.)

Still weighing the switch? Let the numbers make the case.

You've read the features. You've seen the differences. Now put your own organization's data into the equation. Most nonprofits on QuickBooks® discover they're spending 2–3× the subscription price in staff time, consultant fees, and compliance risk they never accounted for. Two minutes with the calculator and the decision gets a lot clearer.

See what QuickBooks® is really costing you →

With the right fund accounting solutions and intentional fund management practices, you can transform your nonprofit’s finances for the better. We'd love to talk to you about how Aplos can improve the way you do accounting. Reach out to us today to start the conversation!