Nonprofit accounting software: Aplos vs QuickBooks Online nonprofit setup

Nonprofit Accounting Software: Aplos vs QuickBooks Online Nonprofit Setup

Managing nonprofit finances requires specialized tools that go beyond typical small business accounting software. Nonprofit organizations must track donations, manage grants, generate fund-specific reports, and comply with specific regulatory requirements. Two popular options that nonprofits often consider are Aplos, a software designed specifically for nonprofits, and QuickBooks Online, a widely-used accounting platform that offers a nonprofit setup.

This article provides a practical comparison of Aplos and QuickBooks Online for nonprofit accounting, focusing on key features, ease of use, reporting, integrations, and pricing to help nonprofit leaders make an informed choice.

1. Purpose-Built Nonprofit Features

Aplos

Aplos was built from the ground up for nonprofits, so it includes features tailored to sector needs right out of the box:

Fund accounting with the ability to track multiple funds separately
Donation tracking with donor management tools and online giving forms
Grant management and reporting
Budgeting tools specific to nonprofit needs
Tax-ready 990 reporting and donation receipts
Event management and partner tracking capabilities

QuickBooks Online (Nonprofit Setup)

QuickBooks Online is a versatile accounting solution that nonprofits can customize with its “nonprofit” chart of accounts template and class tracking features to mimic fund accounting:

Supports multiple income streams through class and location tracking
Customizable chart of accounts can be set up for fund or program tracking
Donation income tracking requires setting up income accounts and classes manually
Generating Form 990 requires exporting data or using third-party integrations
Expense tracking and bank reconciliation are robust

Summary: Aplos offers nonprofit-specific features by default, whereas QuickBooks Online requires some setup and customization.

2. Ease of Use and Setup

Aplos

User-friendly interface tailored to nonprofit terminology
Guided setup specifically designed for nonprofit workflows
Built-in dashboards that track fund balances and donation campaigns clearly
Minimal accounting knowledge required to start using effectively
Customer support familiar with nonprofit issues

QuickBooks Online

Familiar accounting interface familiar to many accountants and small businesses
Requires deliberate setup for nonprofit tracking; can be complex for users unfamiliar with accounting
Learning curve higher around fund accounting and donation tracking
Robust help and training resources broadly applicable but less sector-specific
Wide community of accountants who know QuickBooks

Summary: Aplos generally offers a smoother onboarding experience for nonprofit staff without a strong accounting background. QuickBooks Online offers more power but requires setup.

3. Fund Accounting and Tracking

Fund accounting — tracking income and expenses by fund or program — is critical for nonprofits to maintain transparency and compliance.

Aplos

Native fund accounting with automated tracking of income, expenses, and budgets by fund
Visual reporting by fund and program with drill-down capabilities
Fund balances updated in real time with compliance to nonprofit accounting standards

QuickBooks Online

Use of classes, locations, and custom accounts to replicate fund accounting
Reporting by class or location requires setup and familiarity
Requires manual checks to ensure fund balances and reports are accurate

Summary: Aplos excels in fund accounting out of the box, while QuickBooks Online offers flexibility but requires setup and diligence.

4. Donor and Donation Management

Tracking donations and managing donor relationships is vital, especially for fundraising campaigns.

Aplos

Integrated donor database tied to donations
Online giving forms and pledge tracking
Automated thank-you letters and tax receipts
Ability to segment donors and track giving history

QuickBooks Online

Donations can be tracked as income with customer records for donors
No dedicated donor management or online giving forms
Third-party donor management or CRM integrations needed for advanced features

Summary: Aplos provides better out-of-the-box tools for donor management; QuickBooks Online relies on integrations for these functions.

5. Reporting and Compliance

Aplos

Built-in nonprofit reporting, including Form 990, Statement of Financial Position, and Statement of Activities
Easy export of reports for auditors and stakeholders
Budget vs actual reports tailored for nonprofits

QuickBooks Online

Comprehensive financial reports available but need setup for nonprofit formats
Form 990 reporting requires exporting data or third-party apps
Capable of custom report creation but may require accounting expertise

Summary: Aplos simplifies nonprofit-specific reporting directly within the software; QuickBooks Online offers more flexibility with potentially higher effort.

6. Integrations and Add-Ons

Aplos

Includes built-in tools for donations, event management, and workflows
Integrates with payment processors, email marketing platforms, and CRM tools geared toward nonprofits

QuickBooks Online

Large ecosystem of integrations across fundraising, payments, payroll, and more
Compatible with most nonprofit CRMs and donor management systems
Ideal for organizations with existing tech stacks that want seamless accounting connections

Summary: QuickBooks Online offers broader integration options, while Aplos integrates selected nonprofit-focused tools natively.

7. Pricing and Scalability

Aplos

Pricing structured around nonprofit use cases, often with tiered plans including donations, fund accounting, and payroll
Good value for small to mid-sized nonprofits needing simple, nonprofit-focused software
Can become costly for larger organizations needing add-ons

QuickBooks Online

Subscription pricing based on features, users, and add-ons
Potentially more affordable entry point if only basic accounting is required
Offers scalability for organizations growing into more complex bookkeeping and multi-user environments

Summary: Aplos is often priced specifically for nonprofit needs with nonprofit-friendly features, while QuickBooks Online’s pricing is flexible and may suit nonprofits needing standard accounting with growth potential.

Conclusion: Which One to Choose?

Choose Aplos if: You want a nonprofit-specific solution that is easy to use, includes fund accounting, donation management, and nonprofit reporting out of the box without complex setup.
Choose QuickBooks Online if: You prefer a highly flexible and widely supported accounting platform, are comfortable setting up nonprofit tracking manually, and plan to integrate with broader financial or donor management tools.

Both platforms serve nonprofit accounting needs but from different angles: Aplos aims to simplify nonprofit financial management with built-in sector features, whereas QuickBooks Online offers a customizable, powerful general accounting tool adaptable for nonprofits with some effort.

Carefully assess your organization’s size, accounting expertise, reporting needs, and technical resources before selecting the best nonprofit accounting software for your mission.