Best Accounting Software for Nonprofits in 2025
Accounting software helps businesses and organizations keep track of money, manage budgets, and follow tax rules. It makes tasks like bookkeeping, creating invoices, and financial reporting easier, so you don’t have to use complicated spreadsheets or do calculations by hand.
Nonprofit organizations have special challenges because they need to track donations, invoices, and payroll. They also need to be very transparent because of the kind of work they do. Making end-of-year financial reports can be very hard if staff and volunteers have to start from scratch and switch between different spreadsheets.
Nonprofit accounting software saves time and resources and reduces mistakes in reports. To help you choose the best system for your organization, we have made a list of trusted software suitable for nonprofits of all sizes.
Our Top 4 Accounting Software for Nonprofits
QuickBooks
Starting from: $17.50 /mo
Free trial available
- Fund tracking, donor management
- Unlimited custom invoices and quotes
- Smart invoicing with automated tracking
Sage
Starting from: $61.92 /mo
Not available
- Grant tracking, budgeting
- Serves over 20K businesses
- Custom solutions by experts
Xero
Starting from: $20 /mo
Not available
- Cloud-based accounting
- Streamline onboarding
- Global bank connectivity
Zoho Books
Starting from: $0 /mo
Free plan available
- Multi-user access
- Accounting A to Z
- Account reconciliation & secured banking
1:QuickBooks
QuickBooks is one of the most popular cloud-based accounting software for small businesses. It is simple, effective, and has everything your business needs — all in one place, on both website and mobile app. It comes with many helpful tools and automations that save time and make managing money easier.
✅ Pros and Cons
| Pros | Cons |
|---|---|
| Secure and powerful cloud-based system | No 24/7 phone support (except Advanced plan) |
| Easy-to-use and customizable dashboard | Payroll costs extra |
| Works well with many other apps | Takes time to learn for beginners |
| Access on computer and mobile |
What QuickBooks Offers
QuickBooks gives you many helpful features depending on the plan you choose:
Simple Start: Track income, expenses, and taxes easily.
Essentials: Add bill payments, time tracking, and multiple currencies.
Plus: Includes inventory tracking, project tools, and budgeting.
Advanced: More users, advanced reports, and automation.
These features help make accounting simple and organized for any type of business.
Features and Tools
Reports and Insights
You can easily make reports like balance sheets and profit/loss statements. Reports can also be exported or shared.
Invoices and Payments
Create and send custom invoices, track payments, and set up reminders. You can include discounts, shipping, and tax in your invoices.
Project Tracking
In the Plus plan, you can track how much profit each project makes and add team members to work on them.
Mileage Tracking
Tracks business miles automatically using your phone’s GPS, so you can easily claim them for tax deductions.
Tax Management (with TurboTax)
QuickBooks connects with TurboTax to help you prepare and file taxes easily. You can also get expert help to make sure everything is correct.
Main Functions
Keeps track of income and expenses
Manages invoices and bills
Creates financial reports
Helps prepare for taxes
Automates tasks like recurring payments and reminders
Supports bank connections for real-time updates
Add-ons and Integrations
QuickBooks offers optional add-ons like Payroll, which helps you manage employee payments, taxes, and benefits.
It also connects with many popular apps like:
PayPal, Square, Shopify, Mailchimp, Salesforce
Bill.com for bill automation
POS systems and mobile payment tools
Performance and Ease of Use
QuickBooks works smoothly with your bank accounts and updates financial data in real time. It can automatically sort expenses and schedule payments.
The design is simple once you get used to it. There are many free guides and tutorials to help beginners. QuickBooks can even set up your account for you if you prefer help.
What Makes QuickBooks Special
Intuit Assist: AI feature that helps with invoicing and categorizing expenses.
Connects easily with many third-party apps.
Strong inventory and project tools.
Works on desktop, web, and mobile.
Final Verdict
QuickBooks is one of the best accounting tools for small and mid-sized businesses. It makes invoicing, reporting, and tax management very simple.
With its automation features, integrations, and strong customer support, QuickBooks saves time and helps you stay organized.
2:Sage
Sage Group, based in the UK, is a big company that makes business software. They provide different kinds of software for accounting, payroll, and payments. They have software for computers and also cloud software made for small and medium business owners.
Pros and Cons
| Pros | Cons |
|---|---|
| Can make separate profiles for employees and accountants | Limited customization |
| Send invoices directly from dashboard | No payroll features |
| Automatically saves and protects data |
Key Features
General Accounting: Ledger, bookkeeping, accounts payable/receivable, income & expense tracking, financial reports
Expense Management: Track expenses, mileage, and recurring costs
Invoicing: Create and send invoices easily
Bank Reconciliation: Automatic matching of bank statements with records
Inventory Management: Track products and stock
Time Tracking & Job Management: Track project progress and time
Add-ons & Integrations: Payments, third-party apps, Google Drive connection
Security: Protects data from fraud
Customer Support
Support via phone, email, and chat
Phone support is 24/7, but chat and email can be slower
Online guides, forums, and Sage University classes are available
Performance & Ease of Use
Works on Windows, Mac, Android, iPhone/iPad, Web
Dashboard is simple and easy to navigate
Cloud-connected desktop software allows working with your accountant anytime, anywhere
Guides and tutorials help beginners learn accounting
Why Sage is Unique
Offers a marketplace with extra tools for project management, cash flow, time tracking, and more
Accept payments online using PayPal or Sage Payment Solutions
Helps businesses manage finances, track expenses, and generate reports efficiently
Final Verdict
Sage Accounting Software is good for small and medium businesses. It makes accounting easy with automated invoices, reports, and add-ons. Beginners can learn using guides and classes. Sage is a reliable and trusted company, so you can confidently manage your finances anywhere in the world.
3:Xero
Xero is one of the most popular online accounting software tools for small businesses and accountants. It helps manage money, create invoices, and track expenses all in one place.
Started in New Zealand, Xero has now become a trusted global brand with more than 3.7 million users worldwide. It connects with over 21,000 banks and financial institutions, making it easy for business owners to manage everything from one dashboard.
It’s cloud-based, which means you can use it anywhere — on your laptop, tablet, or phone — without installing anything.
Pros and Cons
| Pros | Cons |
|---|---|
| Smart and helpful built-in assistance | Interface design could be better |
| Uses artificial intelligence for faster work | No inventory assembly feature |
| Gives clear business insights | Time logs not linked to projects |
| Manages client data efficiently |
Features and Tools
Multi-Currency Invoicing
Xero lets you send and receive payments in different currencies. This is perfect for global businesses and automatically adjusts exchange rates.
Custom Reports and Dashboards
You can create your own financial reports and view real-time data in colorful dashboards. It helps you understand your business health at a glance.
Audit Trail
Every change in your account is recorded, so you can always see who did what — keeping your records safe and transparent.
Payment Integration
It connects with Stripe, PayPal, and other gateways, helping you get paid faster and improving cash flow.
Tax and Accountant Collaboration
You can easily create tax reports, manage VAT, and even invite your accountant to work directly on your Xero account. Both of you can view and edit in real time.
Add-ons and Integrations
Xero connects with many other apps to make your work easier.
Popular Add-ons:
Payment gateways (Stripe, PayPal, GoCardless)
Payroll system (Xero Payroll or Gusto)
Project tracking tools (WorkflowMax)
Time tracking (Harvest, TSheets)
Integrations include:
Expensify for expense management
Salesforce and Insightly for CRM
Zapier for automating workflows
Supported Devices
You can access Xero from almost any device or system:
✅ Windows
✅ Mac
✅ Android
✅ iPhone/iPad
✅ Linux
✅ Web browser
Ease of Use
Xero is easy to start and simple to learn. Since it’s cloud-based, there’s no need to install anything — just create an account and begin.
The interface is clean and modern, designed even for people who aren’t accountants. The dashboard shows all important numbers like bank balances, invoices, and cash flow in one place.
If you’re new, Xero offers free training videos, webinars, and online courses (Xero U) to help you learn step by step.
Final Verdict
Xero is a powerful, flexible, and beginner-friendly accounting software for all kinds of businesses. Its cloud-based setup, automation tools, and strong integrations make managing money simple and fast.
Whether you’re a freelancer, small business owner, or running an international company — Xero makes accounting smarter and easier in 2025.
4:Zoho Books
Zoho Books is online accounting software that helps you manage your money, automate business tasks, and work with your team easily. It is affordable and has many features, making it perfect for keeping all your accounting in one place.
Pros and Cons
| Pros | Cons |
|---|---|
| Affordable plans | Not good for very large businesses |
| Can add extra services | Need separate accounts for multiple businesses |
| Easy to use on desktop and mobile | No payroll service add-on |
| Saves time with automation |
Strengths
Good features for invoices, expenses, and reports
Easy to use and mobile-friendly
Affordable and scalable
Automation saves time
Works well with other Zoho apps and third-party apps
Areas to Improve
Inventory management may not be enough for complex businesses
Premium plans might be expensive for small businesses
Advanced features may take time to learn
Customer Support
Phone support: Monday–Friday, 24 hours, free and unlimited
Live chat & email: 24/7
Help center with answers to common questions
Features
Main Features
Invoicing & Receivables: Make professional invoices, set recurring bills, multi-currency, payment reminders, client portal.
Expense Tracking & Payables: Track expenses, attach receipts, manage vendors, schedule payments.
Banking & Reconciliation: Connect multiple bank accounts and credit cards, auto bank feeds, match transactions.
Inventory Management: Track stock, set reorder points, see real-time stock reports.
Reporting & Analytics: 70+ reports, profit & loss, cash flow, balance sheet.
Automation & Workflows: Recurring invoices, payment reminders, email alerts, custom workflows.
Tax Compliance: Tax calculations, filing, VAT & GST support.
Other Features & Add-Ons
Extra users: $2 per month per user or $20 yearly
Send hard copy invoices: $2 per credit
Auto-scan receipts: $5/month or $40/year, up to 50 scans per month
Payment processor integration: Square, Stripe, PayPal
Works with hundreds of apps: Uber for Business, G Suite
Supported Devices
| Device | Supported |
|---|---|
| Windows | ✔ |
| Mac | ✔ |
| Android | ✔ |
| iPhone/iPad | ✔ |
| Web | ✔ |
| Linux | ❌ |
Performance & Ease of Use
Very easy to use for both beginners and accountants
Mobile app lets you manage finances anywhere
Works well with other Zoho apps
Final Verdict
Zoho Books is a great choice for small and medium businesses. It is easy to use, has many helpful features, and affordable plans. Automation helps save time, and both desktop and mobile apps are very user-friendly.
The Importance of Accounting Software for Nonprofits
Nonprofits exist to help people, support communities, and make a positive difference. But to continue doing that work, they must manage money carefully. Nonprofits receive money from many different places, such as donations, membership fees, fundraising events, and grant programs. Some of this money may be given for a specific purpose, and must be used exactly the way the donor or grant-maker requires.
If a nonprofit tries to track everything using paper records or spreadsheets, mistakes can happen. This can lead to confusion, lost funds, and difficulty showing where the money went. That is why accounting software is so valuable. It helps keep all financial information organized in one place and ensures that the organization stays transparent and trustworthy.
In simple terms, accounting software helps nonprofits:
Keep track of every dollar that comes in and goes out.
Show clear financial reports to donors and board members.
Stay organized and avoid mistakes.
Spend money wisely to support their mission.
Key Benefits of Accounting Software for Nonprofits
1. Automatic Tracking of Donations and Grants
Accounting software automatically records donations, grant money, and how those funds are used. This means you don’t have to enter everything by hand. It reduces the chance of errors and keeps your records accurate.
2. Helps with Budgeting and Planning
Every nonprofit has goals and programs they want to run. The software helps you see how much money is available and how it should be used. This makes it easier to plan budgets, avoid overspending, and make smart decisions.
3. Easy Reporting and Compliance
Nonprofits often need to create reports for:
Donors
Board members
Grant organizations
Tax and legal agencies
Accounting software can create these reports in seconds. This saves a lot of time and ensures the reports are correct and easy to understand.
4. Builds Trust and Transparency
Donors and supporters want to know that their money is being used wisely. With clear reports and records, your nonprofit can show exactly where funds are going. This builds trust, which can lead to continued donations and support.
5. Saves Time and Reduces Stress
When financial work is automated, staff members spend less time updating spreadsheets and fixing mistakes. This allows your team to focus on helping your community, not just managing paperwork.
How to Choose the Best Accounting Software for Your Nonprofit
Choosing the right software is important. Here are some simple steps to help you decide:
1. Understand Your Needs
Think about what your nonprofit does. Do you need basic bookkeeping? Do you track many donors? Do you need grant reporting? List your needs before choosing software.
2. Look for Nonprofit Features
Make sure the software can:
Track different types of funds
Record donations
Create nonprofit-friendly reports
3. Make Sure It’s Easy to Use
Choose software with a clean and simple design. Your team should be able to learn it quickly without hours of training.
4. Check Compatibility
Your accounting software should be able to work with:
Donor management systems
Payroll systems
Online payment tools
This helps keep everything connected and organized.
5. Compare Costs
Find software that fits your budget. Many offer special discounts for nonprofits, free versions, or trial periods.
6. Read Reviews and Try It Out
Look at what other nonprofits say about the software. And always try the free demo to see if you like how it works.
Final Thoughts
Good financial management is the foundation of a strong nonprofit. The right accounting software makes this work easier, faster, and more accurate. It helps track donations, manage spending, and create clear reports—all while reducing stress and saving time.
When your finances are organized, you can focus more on the mission that truly matters: helping others and creating positive change.
A nonprofit that manages its money well becomes stronger, more trusted, and more capable of making a meaningful impact.