Today, many nonprofits still wrestle with outdated spreadsheets or for-profit tools that cannot track restricted funds, manage grants, or file IRS Form 990s. With over 1.8 million nonprofits registered in the U.S. according to insights by Cazoomi, the need for the best accounting software for nonprofits is rising fast.
These tools not only support fund accounting and donor tracking but also integrates with CRMs, payroll systems, and fundraising tools to simplify workflows.
If you need the best accounting software for small nonprofits or the best accounting software for large nonprofits, you will discover the best accounting software for nonprofits that fits your budget and scales with your vision in this guide.
Key Takeaways
- Nonprofit accounting software helps manage funds, donors, and compliance with ease.
- Look for tools with grant tracking, budgeting, and built-in IRS Form 990 support.
- Choose software that fits your nonprofit’s size, goals, and reporting needs.
- Explore free and paid options as many offer trials to help you find the right fit.
What Are Nonprofit Organisations?
Nonprofit organisations (also known as not-for-profits) are entities that operate for a social, educational, charitable, religious, or cultural purpose rather than for profit.
Unlike traditional businesses, nonprofits reinvest any surplus revenue into their mission-related activities instead of distributing it to owners or shareholders.
In the United States, nonprofits can qualify for tax-exempt status under Section 501(c)(3) of the Internal Revenue Code. This means they are not required to pay federal income taxes, provided they adhere to regulations such as transparent financial reporting, mission alignment, and public benefit.
Examples of nonprofit organisations include:
| Type of Nonprofit | Description |
|---|---|
| Charitable Organisations | Serve humanitarian goals like poverty relief, disaster aid, or medical access. |
| Educational Institutions | Include schools, scholarship funds, and learning centres. |
| Religious Organisations | Churches, synagogues, mosques, and faith-based groups. |
| Foundations | Grantmaking bodies that fund other nonprofit initiatives. |
| Advocacy Groups | Promote social, environmental, or political causes. |
| Cultural Institutions | Museums, theatres, music academies, and heritage organisations. |
To maintain their tax-exempt status and public trust, nonprofits must keep meticulous records of how they receive and spend funds, making bookkeeping software for nonprofits a mission-critical tool for financial accountability and compliance.
See Also: I Tested The Best Free AI Tools For Accounting – A Comprehensive Guide
Why Nonprofit Accounting Is Unique
Accounting for nonprofit organisations differs significantly from for-profit business accounting because the goals, stakeholders, and compliance needs are fundamentally distinct.
While businesses are driven by profits and investor returns, nonprofits are mission-driven, donor-funded, and focused on accountability and impact.
These are the things that makes nonprofit accounting unique:
| Area | What It Means for Nonprofits |
|---|---|
| Fund Accounting (FASB 116/117) | Tracks restricted and unrestricted funds separately using fund accounting. Each fund acts like a mini-budget tied to donor intent. |
| Financial Reporting & Compliance | Requires detailed reports like the Statement of Activities and Statement of Financial Position. In some regions like the U.S., legal filings such as IRS Form 990 are mandatory. |
| Restricted vs Unrestricted Funds | Helps manage different types of contributions; some with specific conditions and timelines, others without. Accurate tracking is key to compliance. |
| Integration with Donor Tools | Must sync with CRMs, fundraising, and donation platforms to maintain accurate data and reduce manual work. |
| Audit Trails & Accountability | Provides clear tracking of all transactions, with access controls and reporting tools that satisfy governance and donor expectations. |
Key Features to Look For in Nonprofit Accounting Software
Choosing the right accounting software starts with understanding the features that truly matter for nonprofit operations.
From fund tracking to audit readiness, these tools should help your organisation manage finances efficiently, stay compliant, and report accurately to donors and stakeholders.
| Feature | Why It Matters for Nonprofits |
|---|---|
| Fund Accounting | Separates funds by donor restrictions, ensuring compliance and transparency. |
| Grant & Donation Tracking | Tracks individual donor contributions, recurring gifts, and grant conditions. |
| Budgeting & Forecasting | Helps manage program budgets, forecast expenses, and allocate resources effectively. |
| Custom Reporting | Generates tailored reports for boards, funders, and regulatory bodies. |
| Compliance Tools | Supports audit readiness, record-keeping, and financial statements aligned with nonprofit standards. |
| Form Filing Support | Simplifies tax and legal submissions such as Form 990 where required. |
| Integration Capabilities | Connects with donor CRMs, payroll systems, fundraising tools, and banking platforms. |
| Cloud Access & Security | Enables remote collaboration with secure, encrypted data storage and user permissions. |
| Scalability & Pricing Options | Offers flexible plans for small charities to large foundations. |
See Also: 7 Best Small Business Accounting Apps Every Entrepreneur Needs
Top 7 Best Accounting Software for Nonprofits
With hundreds of financial tools available, choosing the right one for your nonprofit can be overwhelming. However, choosing the best accounting software for nonprofits is about matching the features to your needs, budget, and goals.
If you are a small community organisation or a national nonprofit, here are seven trusted tools worth exploring:
1. Aplos
As one of the most trusted platforms in the nonprofit ecosystem, Aplos offers a cloud-based, fund-first accounting solution designed to simplify financial management for organisations of all sizes.
Recognised for its purpose-built approach, it supports everything from fund accounting, donor management to financial reporting, making it ideal for mission-driven teams seeking clarity and compliance.
Its flexible pricing and nonprofit-focused features make it ideal for both new and growing mission-driven teams.
Key Features
| Feature | Details |
|---|---|
| Fund Accounting | Manages restricted vs unrestricted funds with a clear chart of accounts. |
| Donation & Event Tools | Supports online giving, text-to-give, event registration, and contribution statements |
| Form 990 e-Filing | Includes built-in support for IRS Form 990-N and 990-EZ, using 990 tags to streamline tax reporting |
| Budgeting & Reporting | Offers fund-based budgeting, dimensional reporting, dashboards, and custom financial reports |
| Integrations | Connects with payroll (Gusto), donor CRMs, PEX cards, and third-party apps |
| User Permissions & Audit | Enables role-based access, audit trails, and board portal capabilities |
| Support & Onboarding | Includes live training, unlimited email/phone support, and accessible nonprofit-focused customer service |
Pricing Plans
| Plan | Monthly Cost | Best For |
|---|---|---|
| Lite | $79/month (50% off first 3 months) | Ideal for small nonprofits or churches needing basic fund accounting |
| Core | $129/month (promo: $64.50 for 3 months) | Greater control with budgeting, payables, receivables, and recurring gifts |
| Advanced | Custom starts at $229/month | Designed for large nonprofits, supports multi-fund, grant, and project accounting |
2. QuickBooks Online for Nonprofits
Ideal for organisations of all sizes, QuickBooks Online for Nonprofits is among the most popular accounting software for nonprofits, combining familiar bookkeeping tools with nonprofit-specific features.
It adapts standard accounting processes, like class-based ledger entries, to support fund accounting, donation tracking, and IRS reporting.
With deep integrations and nonprofit discounts, it scales easily, making it a great bookkeeping software for small nonprofits and also one of the best accounting software for large nonprofits.
Key Features
| Feature | Details |
|---|---|
| Fund & Class-Based Accounting | Tags funds using classes and locations to separate restricted/unrestricted accounts. |
| Donation Tracking | Tracks individual donor gifts and integrates with fundraising tools like Donorbox, Kindful. |
| Nonprofit Reporting Templates | Offers P&L by Fund/Class, Balance Sheet by Fund, Budget vs Actuals, and Donor Contribution Reports. |
| Form 990 Preparation Support | Tracks the necessary financial data needed for IRS Form 990 and other year-end compliance. |
| Custom Dashboards & Forecasting | Real-time budget comparison, forecasting, and financial visualisation (Advanced plan). |
| App Integrations | Connects with 700+ apps, including CRMs, payroll, and fundraising platforms. |
| User Permissions & Access | Manage role-based access for finance teams, admins, and volunteers. |
Pricing Plans (Via TechSoup Partnership)
QuickBooks offers special nonprofit pricing through TechSoup, a nonprofit technology platform that connects eligible organisations with discounted tools and services.
| Plan | Annual Cost via TechSoup | Users Supported | Best For |
|---|---|---|---|
| QuickBooks Online Plus | US $75–80 (admin fee) | Up to 5 users | Small to mid-sized nonprofits managing donations, budgeting, and fund tracking |
| QuickBooks Online Advanced | US $160–170 (admin fee) | Up to 25 users | Larger nonprofits needing custom dashboards, deeper insights, and advanced permissions |
Eligible organisations can apply through TechSoup.org, receive instant access once approved, and renew their plan each year. New users can also take advantage of a 30-day free trial through QuickBooks before committing to a full subscription.
This collaboration with TechSoup makes QuickBooks one of the most cost-effective accounting software options for nonprofits, combining robust tools with a nonprofit-friendly budget.
See Also: 15 Best Accounting Software for Small Businesses to Track Business Cash Flow
3. Sage Intacct
As a leading cloud-based fund accounting and ERP solution, Sage Intacct delivers powerful tools for mission-driven organisations.
From grant tracking to multi-entity accounting, real-time dashboards, and automated compliance, it is often regarded as the best accounting software for large nonprofits seeking transparency, scalability, and financial control.
Around 32% of Sage Intacct’s 13,000+ customers are nonprofits; a testament to its tailored features and deep focus on the nonprofit sector
Key Features
| Feature | Details |
|---|---|
| Fund Accounting & Multi-Dimensional GL | Supports restricted, unrestricted, and temporarily restricted funds with flexible tagging and dimensions like program, location, and grant. |
| Grant Tracking & Billing | Automates grant revenue recognition, billing schedules, and audit-ready reporting . |
| Automated Compliance Reporting | Includes FASB and Form 990-ready statements, audit trails, and GAAP-standard financials . |
| Real-Time Dashboards & Reporting | Offers custom dashboards and drill-down analytics for diverse stakeholders . |
| Revenue Recognition | Handles complex conditions and long-term grants via ASC 606 automation . |
| Integrations & API | Connects with Salesforce, ADP, Avalara, and other nonprofit tools . |
| Scalable Architecture | Supports consolidation across multiple entities, currencies, and global operations. |
Pricing Overview
Sage Intacct pricing is custom-based, tailored to each organisation’s size, user count, and required modules. Below is a breakdown of the pricing estimates based on research:
| Package / Module | Estimated Annual Cost (USD) | Details |
|---|---|---|
| Core Financials (Base Package) | $9,000–$15,000 | Includes general ledger, AP/AR, cash management, and two legal entities |
| Grants Tracking & Billing | $8,880 (add-on) | Automates fund tracking, billing, and compliance reporting for grant funds |
| Advanced Modules | $3,000–$10,000+ per module | Includes Revenue Recognition, Multi-Entity, Dimensions, Fixed Assets, etc. |
| Typical Total Annual Cost | $15,000–$35,000+ | Depends on number of users, modules, entities, and integrations |
| Implementation & Training | 1.0–1.5× annual subscription | Billed separately by certified Sage Intacct partners for onboarding |
4. Blackbaud Financial Edge NXT
Blackbaud Financial Edge NXT is a cloud-based, fund-first accounting platform designed specifically for nonprofit organisations. It is recognised as one of the best accounting software for large nonprofits, offering robust tools for fund, grant, and project accounting.
Organisations that need advanced budgeting, audit-grade trails, and seamless integration with fundraising CRMs often turn to Blackbaud for its nonprofit-centric approach.
Key Features
| Feature | Details |
|---|---|
| Fund & Grant Accounting | Tracks restricted funds, grants, awards, and activities per fund without inflating the chart of accounts. |
| Automated Reconciliation & Expense Controls | Speeds up bank and credit card matching and automates expense submission with budget checks. |
| Detailed Grant & Project Management | Stores grant-specific data (contacts, milestones, budgets), automates reimbursements, sets alerts and deadlines. |
| Custom Dashboards & Reporting | Includes Visual Chart Organiser and Insight Designer for stakeholder-ready visuals. |
| Audit Trail & Access Control | Offers view-only licenses, internal control settings, and comprehensive audit logs. |
| CRM Integration | Seamless sync with Raiser’s Edge NXT and other fundraising and ERP tools via SKY API. |
Pricing Overview
Blackbaud does not publish set prices; instead, licences are scaled to your organisation’s size, module needs, and integration requirements.
While it is more expensive than other basic tools, it offers exceptional value for larger nonprofits requiring advanced fund and grant accounting features.
| Component | Estimated Annual Cost (USD) | Details |
|---|---|---|
| Core Fund Accounting Package | Custom pricing; generally high | Includes general ledger, AP/AR, and cash management |
| Grant & Program Module | Included or additional (likely 5-10% of base) | Enables budgeting, reimbursements, and grant tracking |
| Add‑on Modules | Varies across modules | Includes dashboards, data extraction, and multi-entity |
| Implementation & Training | Typically billed separately | Custom pricing, generally high |
5. NonprofitPlus
Built on the powerful Acumatica ERP platform, NonprofitPlus is a comprehensive cloud-based accounting and financial management suite designed specifically for mission-driven organisations.
It offers enterprise-level functionality like fund accounting, grant tracking, procurement, and project-based budgeting, all with unlimited users and mobile access.
With its deep nonprofit focus, it is a strong contender for those seeking robust tools without per-user cost scaling
Key Features
| Feature | Details |
|---|---|
| Fund & Grant Accounting | Built-in tools for managing restricted/unrestricted funds and grant cycles |
| Encumbrance & Budget Controls | Real-time budget checks with spending limits programmed into workflows |
| Procurement & Financial Suite | Full module set: AP/AR, GL, cash, fixed assets, time/expense tracking |
| Mobile & Unlimited Users | Includes a mobile app; pricing is independent of user count |
| Audit Trail & Permissions | Detailed logs, secure access controls, and role-based permissions |
| CRM and ERP Integration | Seamless integration with Salesforce and other major systems via Acumatica |
Pricing Overview
NonprofitPlus offers a starting price of approximately US$675/month, which covers robust ERP-grade functionality suitable for growing and mid-sized nonprofits.
Consultations and implementation services are provided by ASI partners, and costs may vary based on deployment complexity and add-ons.
| Plan / Module | Estimated Monthly Cost (USD) | Details |
|---|---|---|
| Base Subscription | $675/month (starting rate) | Full access to core accounting and financial modules |
| Unlimited Users & Mobile App | Included | No extra cost per user or mobile access |
| Optional Add-ons | Variable | Additional modules (e.g. advanced procurement, inter-company) via A |
6. File 990
File 990 is a streamlined, IRS-authorised e‑filing platform specialising in submitting Forms 990‑N, 990‑EZ, and full 990.
Designed for small to mid-sized nonprofits, it simplifies tax compliance by importing your EIN, autofilling data, and providing real-time IRS acceptance, making it an essential free bookkeeping software for nonprofits focused on annual filings.
Key Features
| Feature | Details |
|---|---|
| Supports 990-N, 990-EZ & Standard 990 | Covers all major IRS 990 forms, including schedules for organisations of varied size |
| IRS Data Import & Error Checks | Automatically pulls organisation info via EIN and flags errors before submission |
| Automated Filing Reminders | Sends notifications ahead of IRS deadlines to keep filings timely |
| Secure e‑Filing & Acknowledgement | Bank-grade encryption, with IRS acceptance confirmations typically within hours |
| Enterprise/Multi-Chapter Dashboard | Allows oversight for organisations with multiple chapters or affiliated entities |
| Role-Based Review Workflow | Enables inviting board members or staff to review before final submission |
| Transparent Pricing & US Support | No hidden costs; live phone/chat support available from U.S.-based teams |
Pricing Overview
With no upfront fees, File 990 lets nonprofits start free and pay per filing, typically 30–90% cheaper than hiring professional accountants.
It is one of the most budget-friendly, best free accounting software programs for nonprofits focused on IRS compliance
| Form Type | Cost per Filing (USD) |
|---|---|
| 990-N (e‑Postcard) | $54.99 |
| 990-EZ | $84.99 |
| Full 990 | Contact File 990 for pricing |
| Enterprise (Multi-Chapter) | Custom pricing |
7. Xero for Nonprofits
Xero, known for its intuitive cloud-based accounting, offers tailored features and special pricing for nonprofit organisations.
It is one of the most popular accounting software programs for nonprofits, offering tools for fund tracking, budgeting, compliance, and seamless third-party integrations, all within a nonprofit-friendly platform.
Key Features
| Feature | Details |
|---|---|
| Fund & Project Tracking | Uses tracking categories to differentiate restricted/unrestricted funds, campaigns, and program spending. |
| Cash Flow Dashboard | Offers a real-time cash status overview with summaries to support budgeting. |
| Customisable Financial Reporting | Creates stakeholder-friendly reports, including donor summaries and board-ready dashboards. |
| Payroll & Expense Management | Supports U.S. payroll through Gusto integration and includes automated bill and expense capture. |
| Cloud Access & Mobile App | Enables remote access and expense approval via Xero’s mobile app. |
| App Integrations | Connects with 1,000+ apps; key integrations include Keela (CRM), Hubdoc (document capture), and Infoodle (donor/volunteer tracking). |
| Compliance Tools | Facilitates IRS readiness with audit logs, restricted fund tracking, and financial export capabilities. |
Pricing Overview
Xero offers three main subscription plans with special nonprofit discounts of up to 25%, making it one of the most affordable cloud-based platforms for charitable organisations.
Nonprofits can access advanced accounting features, including fund tracking and reporting, at reduced monthly rates once eligibility is verified through Xero Central.
| Plan | Standard Price (USD) | Discounted Nonprofit Price | Best Suited For |
|---|---|---|---|
| Early | $29/month | Approximately $21/month | Very small or grassroots nonprofits |
| Growing | $47/month | Approximately $35/month | Small to mid-sized charitable entities |
| Established | $80/month | Approximately $60/month | Larger nonprofits with complex needs |
All Xero plans include a 30-day free trial. The nonprofit pricing is applied after verification and includes key features like bank reconciliation, basic reporting, cloud access, and integrations with tools such as Gusto for payroll and Hubdoc for document capture.
For larger organisations, optional modules like multi-currency support and advanced analytics are available on demand, enabling full scalability across growth stages.
Side-by-Side Comparison of Our Top Picks
This comparison gives a high-level view to help nonprofits choose the tool that aligns with their size, budget, and operational needs.
| Software | Best For | Starting Cost (USD) | Key Standout Features | Free Trial |
|---|---|---|---|---|
| Aplos | Small to mid-sized nonprofits | $79/month (50% off 1st 3 months) | Fund accounting, donation tools, 990 prep | Yes (15 days) |
| QuickBooks Online | Small to large nonprofits via TechSoup | $75/year (Plus), $160/year (Advanced) | Class-based tracking, nonprofit reports, 700+ integrations | Yes (30 days) |
| Sage Intacct | Large, complex nonprofits | $9,000/year (custom pricing) | Multi-entity fund accounting, grant billing, and dashboards | No |
| Blackbaud Financial Edge NXT | Large foundations and NGOs | Custom (high-end) | Deep fund/grant control, CRM sync, audit-ready reports | No |
| NonprofitPlus | Mid-sized nonprofits needing ERP-level tools | $675/month | Unlimited users, full ERP suite, Acumatica base | No |
| File 990 | Small nonprofits focused on tax filing | $54.99 per 990-N | IRS-authorised e-filing, real-time acceptance, and filing reminders | Start free |
| Xero | Small to mid-sized nonprofits | $21–$60/month (with discount) | Real-time dashboards, 1,000+ integrations, donation tracking | Yes (30 days) |
How to Choose the Right Tool
Choosing the best accounting software for your nonprofit is not just about picking a brand; it is about matching your organisation’s operational and financial needs with the right capabilities.
Here are the most important criteria to guide your selection process:
| Decision Factor | What to Consider |
|---|---|
| Compliance Requirements | Ensure the tool supports IRS Form 990, FASB standards, and audit-friendly reporting |
| Scalability | Pick software that can grow with your funding sources, team size, and program scope |
| Integration Capabilities | Look for built-in compatibility with CRMs, donation platforms, and payroll systems |
| Trial and Evaluation | Use free trials and live demos to assess usability, setup time, and core functions |
| Nonprofit Discounts | Check if you qualify for access to nonprofit discounts to reduce long-term software costs. |
Implementation Tips for Nonprofits
A smooth rollout can make or break your accounting software’s effectiveness. To get the most out of your investment, nonprofits should prepare the right structure, access, and training from day one.
| Implementation Task | Execution Strategy |
|---|---|
| Chart of Accounts Preparation | Clean and customise your accounts to reflect programs, departments, and fund types |
| Fund/Program Segmentation | Define clear tracking categories for grants, restricted funds, and functional areas |
| User Role Assignments | Set access levels by role, board, volunteer, and finance staff for secure collaboration |
| Staff Onboarding & Training | Schedule guided training sessions using vendor resources and live demos |
| Annual Review & Optimisation | Reassess software usage yearly; scale features or restructure reporting as needed |
Conclusion
Choosing the best accounting software for nonprofits is a strategic decision that directly affects how effectively your organisation can manage funds, remain compliant, and report to stakeholders.
With unique accounting needs like fund separation, grant tracking, and IRS obligations, nonprofits must go beyond general-purpose tools.
Test thoroughly, review annually, and never underestimate the long-term impact of choosing the right system.
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Frequently Asked Questions (FAQs)
What is the best accounting software for a nonprofit?
The best accounting software for a nonprofit depends on your size and specific needs. Aplos is ideal for small to mid-sized nonprofits, while QuickBooks Online (via TechSoup) offers strong value and flexibility.
Larger organisations may prefer Sage Intacct or Blackbaud Financial Edge NXT for advanced fund and grant accounting.
What is the best accounting method for nonprofit organisations?
Nonprofits typically use fund accounting, which focuses on tracking funds by their source and purpose (e.g. restricted, unrestricted). This method ensures transparency, compliance with donor restrictions, and accurate reporting aligned with standards like FASB 116 and 117.
Is QuickBooks free for nonprofits?
QuickBooks is not free, but it offers deeply discounted pricing for eligible nonprofits through TechSoup. Plans like QuickBooks Online Plus and Advanced are available for as low as $75–160 per year, compared to retail rates of $90–$200 per month.
What is the difference between QuickBooks and QuickBooks Nonprofit?
“QuickBooks Nonprofit” is not a separate product, but rather a customised setup of QuickBooks Online or Desktop. It includes a nonprofit-specific chart of accounts, reports like P&L by fund, and class tracking to simulate fund accounting.
Can small nonprofits use free accounting software?
Yes. Tools like Wave, ZipBooks, and File 990 (for tax filing) offer free or low-cost solutions suitable for small nonprofits with simple accounting needs. However, they may lack fund accounting, donation tracking, or audit support found in paid tools.
Do nonprofits need special accounting software?
Yes. Unlike for-profits, nonprofits must track restricted vs. unrestricted funds, comply with IRS Form 990, and maintain transparency with donors and boards. Specialised software simplifies this through fund accounting, grant tracking, and nonprofit-specific reports.
Is Xero good for nonprofits?
Yes. Xero offers nonprofit-specific discounts and features like donation tracking, fund segmentation, and real-time cash flow dashboards. It’s a solid choice for small to mid-sized nonprofits looking for cloud-based financial management.
