Aplos vs. QuickBooks Nonprofit: Which tool is best? [2026]

Choosing between Aplos and QuickBooks Nonprofit comes down to what you value more: a specialized tool built from the ground up for nonprofits, or a powerful, all-purpose accounting platform adapted for nonprofit use. Aplos offers intuitive fund accounting and donation management designed for users with little accounting know-how. In contrast, QuickBooks Nonprofit provides a robust, scalable accounting system with an extensive ecosystem of integrations, but it requires more customization to handle nonprofit-specific needs.

What is Aplos?

Aplos is a cloud-based accounting and donor management software created specifically for the workflows of nonprofit and church organizations. It prioritizes simplicity and compliance, focusing entirely on fund accounting, which is the practice of tracking financial resources by their designated purpose (e.g., unrestricted, temporarily restricted, permanently restricted funds). The platform is designed to be user-friendly, allowing staff and volunteers without a formal accounting background to manage finances, track donations, generate acknowledgments, and prepare required financial statements and compliance reports like the Statement of Financial Position and Form 990.

What is QuickBooks Nonprofit?

QuickBooks Nonprofit is not a standalone product but rather a specialized chart of accounts and configuration of QuickBooks Online, the world's most popular small business accounting software. It adapts the powerful features of QuickBooks—such as invoicing, accounts payable, bank reconciliation, and payroll—for the nonprofit sector. While it's a general accounting platform at its core, it uses features like classes and tags to facilitate fund accounting and grant tracking. Its main advantage is its familiarity, massive integration marketplace, and the large number of accountants and bookkeepers certified in its use.

Comparing Aplos vs. QuickBooks Nonprofit

Both platforms can get the job done for a nonprofit, but their approach, strengths, and ideal user profiles differ significantly. Aplos leads with purpose-built simplicity for fund accounting, whereas QuickBooks offers more versatility and scalability.

Comparison Area

Aplos

QuickBooks Nonprofit

Core Focus

True fund accounting built specifically for nonprofits and churches.

General business accounting adapted for nonprofits via classes and tags.

Fund & Restricted Funds

Designed for tracking restricted and unrestricted funds intuitively. Clear separation and reporting.

Accomplished through workarounds like using the "Class" or "Location" features. Less intuitive and requires disciplined data entry.

Donation & Grant Tracking

Includes a built-in donor management system for tracking contributions, generating donation receipts, and running donor reports.

Basic sales receipts can track donations, but robust features require integration with third-party donor management apps.

Financial Reporting

Generates nonprofit-specific reports out-of-the-box (e.g., Statement of Financial Position, Statement of Activities, Form 990 data).

Offers strong standard business reports, with nonprofit-specific versions available. Customization is often needed.

Ease of Use

Considered more user-friendly, especially for non-accountants, due to its nonprofit-centric language and workflows.

Can have a steeper learning curve for users without traditional accounting knowledge. Requires setup and customization.

Integrations

Has a limited number of native integrations. Focuses on being an all-in-one platform.

Vast ecosystem with hundreds of third-party app integrations for payment processing, CRM, payroll, and more.

Scalability

Best for small to mid-sized nonprofits. May not support the complexity of very large, multi-entity organizations.

Highly scalable, with different tiers (Plus, Advanced) to support organizational growth and increasing complexity.

Pricing

Starts around $59/month. Additional modules for features like advanced fundraising can increase the cost.

Starts around $30/month for the Plus plan. Price increases for advanced features, payroll, and the number of users.

Fund Accounting and Restricted Funds

This is where Aplos truly shines. The platform is built on a true fund accounting framework. From the moment you set it up, you can create and manage separate funds without complicated workarounds. Reporting on the use of restricted grants or designated donations is straightforward because the system is designed to keep these funds segregated. This structure reduces the chance of human error and makes audit preparation much simpler.

QuickBooks Nonprofit handles fund accounting by repurposing other features, most commonly "Classes." You can assign each transaction to a specific class (e.g., "General Fund," "2026 Building Grant," "Annual Gala"). This method works and can be effective if used consistently, but it isn't a native function. It puts the burden on the user to accurately tag every single transaction. For organizations with complex grant restrictions, this can become cumbersome and error-prone.

Donation Management

Aplos includes donation management as a core part of its offering. You can track individual donors, record pledges, send automated giving statements, and manage fundraising campaigns directly within the accounting software. This integration means your financial records and fundraising data are always in sync, providing a clear picture of your organization's financial health without needing a separate system.

QuickBooks can record incoming donations using its sales receipt feature, but it lacks dedicated donor management tools. To get functionality comparable to Aplos, you’ll need to integrate a third-party donor management or CRM application like Bloomerang, Little Green Light, or Kindful. While this offers flexibility, it also adds another subscription cost and requires maintaining an integration between two systems.

Reporting and Compliance

Aplos is designed with nonprofit compliance in mind. It can generate board-ready reports like the Statement of Activities and Statement of Financial Position with the correct formatting from day one. It also has features specifically to help prepare data for IRS Form 990, streamlining the tax filing process.

QuickBooks Online has a robust reporting engine but it speaks the language of for-profit business. While the Nonprofit plan provides a template for reports like a "Statement of Financial Income and Expense," you will often need to do more customization to make them ready for your board or funders who are expecting standard nonprofit formats. Preparing for a Form 990 is also more manual, requiring you to pull data from various reports and organize it yourself.

Ease of Use and Ecosystem

For volunteers or staff without formal accounting training, Aplos is generally easier to learn. The terminology and workflows are tailored to nonprofits, which flattens the learning curve. However, because it's a smaller, niche product, finding bookkeepers or accountants who specialize in Aplos can be more challenging.

QuickBooks has a steeper learning curve because it is built around standard double-entry accounting principles. However, an enormous advantage is its market dominance. Millions of bookkeepers, CPAs, and accounting professionals are experts in QuickBooks. It's easy to find help, access training resources, and integrate with hundreds of other business apps you might already use.

Which One Should You Choose?

The right choice depends entirely on your organization’s priorities, size, and existing technical capabilities. One is not definitively better than the other; they simply serve different needs.

Choose Aplos if:

• Fund accounting is your top priority. If your organization manages multiple restricted grants and designated funds, Aplos’s native fund accounting will save you time and reduce errors.
• Your staff includes non-accountants. Its straightforward interface and nonprofit-specific language make it easier for program managers, executive directors, or volunteers to use.
• You are a church or faith-based organization. Aplos has features explicitly designed for church finance, such as tracking tithes and offerings.
• You want an all-in-one solution. If you prefer to have your accounting and donor management in a single, integrated platform, Aplos provides that out of the box.

Choose QuickBooks Nonprofit if:

• You need a highly scalable platform. As your nonprofit grows, QuickBooks can grow with you through its advanced tiers and vast feature set.
• Integrations are important. If you need your accounting software to connect seamlessly with a specific CRM, payment processor, or other specialized app, QuickBooks’s enormous app marketplace is a major advantage.
• Your accountant or bookkeeper already uses QuickBooks. Sticking with the platform your financial pro already knows can save significant time on training and implementation.
• You have complex general accounting needs. If your organization runs complex payroll, manages inventory, or bills for services, the core functionality of QuickBooks is more powerful than Aplos.

Final Thoughts

Ultimately, your decision comes down to a choice between a specialized expert and a powerful generalist. Aplos is the specialized expert, built entirely for nonprofits and churches with a deep understanding of fund accounting. QuickBooks Nonprofit is the powerful generalist, adapting a best-in-class accounting engine for the nonprofit world through customization and integration.

Regardless of which platform you select, staying on top of nonprofit regulations and tax compliance is key. For tough questions around Form 990 reporting, unrelated business income tax (UBIT), or complex state filing requirements, dedicated research is often necessary. This is where AI-powered tools can supplement your software, as platforms like Feather AI deliver instant, citation-backed answers directly from authoritative sources like the IRS tax code, helping your team ensure compliance without hours of manual research.