Are your funds truly audit-ready?
Managing restricted funds and grants with generic tools creates compliance headaches and wastes hours of your team’s valuable time.
These manual workarounds and spreadsheets lead to costly accounting errors that put your organization’s reputation and crucial funding at serious risk.
A study by the University of Notre Dame found nonprofits have accounting error rates almost twice that of for-profits. This highlights how easy it is to make mistakes without the proper system.
The right software is built to simplify your fund accounting and automate compliance, making audits far less stressful for your entire team.
Speaking of fund accounting, my guide on best fund accounting software covers everything you need to know.
In this guide, I’ll walk you through the best nonprofit accounting software to help you find a tool that fits your unique operational needs and budget.
You’ll discover how to maintain compliance, streamline reporting, and gain the financial clarity needed to grow your mission and donor trust.
Let’s dive in.
Quick Summary:
| # | Software | Rating | Best For |
|---|---|---|---|
| 1 | Aplos → | Small to mid-sized nonprofits | |
| 2 | MIP → | Complex nonprofits with many funds | |
| 3 | QuickBooks → | Growing nonprofits and teams | |
| 4 | FreshBooks → | Small nonprofits and startups | |
| 5 | Cougar Mountain Software → | Small to mid-sized nonprofits |
1. Aplos
Struggling with complex nonprofit financial management?
Aplos offers a cloud-based platform designed specifically for your organization’s unique accounting and operational needs. This means you can track multiple funds with clarity.
The software includes true fund accounting, which is crucial for managing restricted funds and ensuring compliance. It helps you accurately handle grants, departments, and specific programs.
Simplify your financial operations.
Aplos makes critical management tasks straightforward, helping you engage donors and prepare essential financial documents effortlessly. You can manage your books and bottom line the right way.
The integrated suite provides prebuilt and customizable real-time financial and contact reports, allowing you to show a clear through-line between resources and impact. This level of transparency is vital for donor trust and internal accountability, giving you insights into how dollars translate to your mission’s impact.
Additionally, Aplos integrates donor management, fundraising tools, and communication features like email marketing and text-to-give. This allows you to accept online donations, manage people and groups, and foster generosity to grow giving, all from one place.
Track funds with clarity.
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Key features:
- True Fund Accounting: Designed for nonprofits and churches, it allows accurate tracking of multiple funds and helps manage grants, departments, and specific programs.
- Integrated Donor Management: Keep track of donors and volunteers with a comprehensive CRM, create custom communication lists, and encourage online and mobile giving.
- Real-time Financial Reporting: Generate prebuilt or customized reports like Balance Sheets and Income Statements by fund, ensuring transparency and easy sharing with boards.
Aplos features, pricing, & alternatives →
Verdict: Aplos stands out as a strong contender for the best nonprofit accounting software by offering an all-in-one solution that addresses the specific challenges of nonprofit financial management, including precise fund tracking and robust reporting. Over 65,000 organizations trust Aplos for its advanced, yet affordable, capabilities.
2. MIP
Struggling with complex nonprofit financial management?
MIP Accounting is a cloud-based, SaaS fund accounting solution designed to track unlimited funds and manage your financial books. This means you can easily monitor and [report your organization’s finances], navigating the complexities of multiple revenue sources and funding requirements. The result is increased efficiency while ensuring your nonprofit stays compliant.
You need a true partner in your financial journey.
MIP Accounting provides best-in-class accounting tools, including a General Ledger, Fund Accounting, Budgeting, and Grant Reporting. Its robust reporting and budgeting capabilities are integrated with configurable dashboards, offering a unique, multidimensional Chart of Accounts. Plus, it handles requisition/purchase order workflows and automation, and even integrates payroll and HRMS with your accounting for comprehensive financial oversight.
This comprehensive software ensures your fiscal stability and effectively manages ever-increasing financial complexities.
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Key features:
- Unlimited Fund Tracking: Track unlimited funds and manage financial books in a streamlined, user-friendly system, perfect for organizations with diverse funding sources.
- Robust Reporting & Budgeting: Gain fiscal stability and ensure compliance with comprehensive reporting, budgeting, and grant reporting capabilities tailored for nonprofits.
- Integrated Modules: Simplify intricate financial processes with integrated payroll and HRMS, AP, AR, and advanced security, all within a single system.
MIP features, pricing, & alternatives →
Verdict: MIP Accounting is a strong contender for the best nonprofit accounting software, specifically designed to address the challenges of complex fund tracking and compliance, ensuring fiscal stability and growth for your organization.
3. QuickBooks
Struggling with complex nonprofit financial management?
QuickBooks offers a unified platform to run your organization, making confident decisions easier. This means you can simplify fund tracking and automate compliance.
You’ll manage cash flow effortlessly, capture receipts on the go, and streamline your invoicing process. This is vital for maintaining transparent financial records and securing donor trust.
Simplify your accounting, empower your mission.
QuickBooks helps your nonprofit by securely importing and organizing transactions automatically, cutting down on tedious tasks. You can also accept various payment methods directly through invoices, getting paid faster.
Additionally, you can generate comprehensive reports like profit & loss statements and balance sheets, giving you clarity on where money is going and coming from. Plus, it allows for multiple users with custom access controls, enabling your team to collaborate while maintaining data security. You can even track project profitability to ensure efficient use of funds.
QuickBooks also automates key workflows and offers financial planning tools, empowering your team to create budgets using real-time data. This integrated approach ensures seamless operations from managing bills to preparing for tax season.
The result is increased efficiency and accurate financial oversight.
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Key features:
- Automated Bookkeeping & Payments: Streamline income and expense tracking, allowing you to accept various payments and get automatic invoice reminders, speeding up cash flow.
- Comprehensive Reporting & Budgeting: Gain clear insights into your nonprofit’s financial health with detailed reports and tools to create budgets for effective financial planning.
- Multi-User Access & Expert Support: Control who sees what data, collaborate with your team, and access expert guidance for setup and bookkeeping whenever you need it.
QuickBooks features, pricing, & alternatives →
Verdict: If your nonprofit seeks a reliable solution for precise fund tracking, efficient grant management, and seamless financial transparency, QuickBooks emerges as a strong contender for the best nonprofit accounting software. Its robust reporting and automated features help reduce administrative burdens, supporting compliance and growth.
4. FreshBooks
Struggling to track nonprofit funds accurately?
FreshBooks offers all-in-one billing, payroll, and accounting features to streamline your financial operations effortlessly.
This means you can easily manage your books, keep stakeholders happy, and stay organized while ensuring compliance and transparency for your nonprofit.
Here’s how to simplify your financial management.
FreshBooks allows you to create professional invoices in minutes, automatically adding tracked time and expenses, calculating taxes, and customizing payment options. This is crucial for precise grant tracking and donor reporting.
You can bill fast, get paid even faster, and automate the rest with recurring invoices, online payments, and late payment reminders. Additionally, keep track of your expenses with mobile receipt scanning, bank account imports, and automated expense categorization, ensuring every dollar is accounted for. Know where you stand in real-time with double-entry accounting tools, powerful financial reports, and easy access for your accountant, which simplifies audits. Plus, with payroll and team management features, your entire organization can collaborate seamlessly, reducing administrative burdens and ensuring everyone is on the same page.
Achieve clear financial visibility.
Key features:
- Comprehensive Financial Tracking: Create professional invoices with automated expense and time tracking, ensuring accurate billing and compliance for restricted funds.
- Automated Payments & Expenses: Bill quickly, automate recurring invoices, and track expenses via mobile receipt scanning and bank imports, simplifying donor and grant accounting.
- Real-time Accounting & Reporting: Utilize double-entry accounting tools and powerful financial reports for real-time insights, making audits and financial transparency straightforward.
FreshBooks features, pricing, & alternatives →
Verdict: FreshBooks stands out as a strong contender for the best nonprofit accounting software due to its all-in-one billing, payroll, and accounting capabilities. You can save up to 553 hours and $7000 annually, demonstrating its efficiency for managing nonprofit finances, ensuring precise fund tracking, and simplifying compliance for growing organizations.
5. Cougar Mountain Software
Struggling to manage nonprofit finances and ensure audit readiness?
Cougar Mountain Software, particularly Denali Fund, offers tailored solutions for transparent fund accounting. This means you can easily track federal, private, and corporate grants.
It’s designed to help your organization stay on top of everything that comes into your system, addressing the critical need for transparency and detailed financial oversight. This ensures you maintain compliance.
Here’s how to simplify your bookkeeping and make audits easier.
Cougar Mountain Software provides a powerful on-premise accounting solution, specifically designed for nonprofits and small to mid-sized businesses. This flexibility means you can choose the platform that best fits your operational needs.
Denali Fund is a bespoke solution to help your nonprofit organization manage all aspects of fund accounting, ensuring you stay transparent with your accounts. This allows for precise tracking of restricted funds, a common pain point for many nonprofits. Additionally, Denali Business offers seamless bookkeeping, while Denali Payroll handles all your payroll complexities, including taxes and regulatory compliances, saving you significant time and effort. The Denali Web component provides in-depth financial analytics, empowering you to make better financial decisions.
You’ll gain comprehensive control over your financial data.
Key features:
- Fund Accounting: Specifically tailored for nonprofits, Denali Fund helps you track federal, private, and corporate grants, ensuring complete transparency and compliance for all incoming funds.
- Flexible Deployment: Denali Accounting is available on both cloud and on-premise platforms, offering you the flexibility to choose the best fit for your nonprofit’s IT infrastructure and operational preferences.
- Comprehensive Payroll Management: Denali Payroll streamlines all aspects of your payroll, including standard pay, special pay, taxes, deductions, and regulatory compliances, saving your team time and effort.
Cougar Mountain Software features, pricing, & alternatives →
Verdict: Cougar Mountain Software is a strong contender for the best nonprofit accounting software, particularly with its Denali Fund module, which directly addresses the complexities of grant tracking and audit preparedness. Its commitment to maintaining an unbreakable audit trail, as mentioned on their homepage, ensures robust financial integrity for your organization.
Conclusion
Is audit season causing you stress?
I get it. Choosing the wrong tool wastes time and risks your mission. Generic software just doesn’t grasp your unique compliance needs.
And that matters. Research shows organizations using dedicated tools report improved financial accuracy and fewer errors. This shift is absolutely critical for maintaining donor trust and securing funding for your programs.
So what’s the best path forward?
From my review, Aplos is the clear winner. Its all-in-one platform is built from the ground up to solve nonprofit accounting challenges.
I love its true fund accounting for simplifying complex grant tracking. It is the best nonprofit accounting software for total compliance and financial clarity.
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I strongly encourage you to start a free trial of Aplos and see how it streamlines your entire financial workflow firsthand.
You’ll gain complete audit confidence.
