Nonprofit Accounting software helps nonprofit organizations manage finances efficiently, ensure regulatory compliance, and make data-driven decisions to maximize their impact.

Nonprofit organizations are driven by a passion to make a difference. However, managing donations, grants, and expenses while ensuring strict financial compliance can be overwhelming. Nonprofit accounting software solutions offer tools to track every penny responsibly and improve donor relations.

After thorough research and hands-on testing, Geekflare came up with this list of software based on nonprofit-related features, usability, and pricing to streamline accounting for a nonprofit organization and safeguard tax-exempt status.

You can trust Geekflare

Imagine the satisfaction of finding just what you needed. We understand that feeling, too, so we go to great lengths to evaluate freemium, subscribe to the premium plan if required, have a cup of coffee, and test the products to provide unbiased reviews! While we may earn affiliate commissions, our primary focus remains steadfast: delivering unbiased editorial insights, and in-depth reviews. See how we test.

Wave Accounting

Wave Accounting

Best for Small Nonprofit Organizations

Geekflare rating score 4.2 out of 5
4.2
|
  • Grant Management
    No
  • Mobile App
    Yes
  • Customer Support
    Email, Live Chat, Help Center

About Wave Accounting

Wave Accounting is the right not-for-profit accounting software for a small or growing charitable foundation. Organizations can become their own accountants and save donation money on additional staff.

Wave works online on popular web browsers. This nonprofit accounting software offers free invoice, accounting, and banking services. Wave was launched in 2010 and now has 250+ employees. In June 2024, it reached $3,000,000,000 in invoice-generated payments.

Wave Accounting Features

  • Key feature

    Online invoicing granting foundations or donors

  • Key feature

    Donors can pay the charity effortlessly and securely through its online payment panel

  • Key feature

    Accepts debit cards, credit cards, Apple Pay, and direct bank transfers

  • Key feature

    Track donations and their utilization in a painless way

  • Key feature

    The accounting module prepares tax reports in the correct format

  • Key feature

    Bank account linking with the accounting books for easy reconciliations

  • Key feature

    Recurring billing and automated credit card payments for repeated donors

  • Key feature

    Dashboard to get all the business stats in one place

Wave Accounting Pros/Cons

  • Advantage

    Auto-merge and categorize transactions

  • Advantage

    Add attachments to invoices and estimates

  • Advantage

    Mobile app for invoicing and estimate

  • Disadvantage

    Payment acceptance and payroll features cost additional charges

  • Disadvantage

    Starter plan does not allow removing wave branding

Wave Accounting Pricing

Wave Accounting offers 2 straightforward plans, as listed below.

PlanPricing (monthly)Offerings
StarterFreeOnline invoice, cash flow management, unlimited estimates
Pro$16Late payment reminders, Track expenses, auto-import bank transactions
MIP Fund Accounting

MIP Fund Accounting

Best for Comprehensive Fund Accounting

Geekflare rating score 4.0 out of 5
4.0
|
  • Grant Management
    Yes
  • Mobile App
    No
  • Customer Support
    Phone, Live Chat, Support Center, Knowledgebase

About MIP Fund Accounting

MIP Fund Accounting is one of the best accounting software for nonprofits. It supports nonprofits, municipalities, tribes, educational, and other organizations. It allows organizations to manage finances and revenue sources with built-in compliance and robust reporting tools.

MIP nonprofit accounting software helps users manage an unlimited number of grants, account for flexible segments, handle restricted and unrestricted funds, and develop insights into the organization. Bill Locklear and Hans E. โ€œRustyโ€ Turley Jr. invented MIP Fund Accounting software in 1982. It serves over 100,000 clients in 30 countries.

MIP Fund Accounting Features

  • Key feature

    Core functionalities such as general ledger, fund accounting, grant reporting, AR, and AP

  • Key feature

    Integrated and configurable dashboard

  • Key feature

    Multidimensional and unique chart of accounts

  • Key feature

    Integrated payroll and HRMS with accounting software

  • Key feature

    Workflows for requisition or purchase order

  • Key feature

    Track finances and manage unlimited funds

  • Key feature

    Transfer general ledger entries from outsourced payroll into MIP

  • Key feature

    Unlimited number of customized budgets, including cross-year budget

MIP Fund Accounting Pros/Cons

  • Advantage

    Manage multiple grantor relationships

  • Advantage

    Advanced security and fraud protection

  • Advantage

    FASB- and GASB-compliant reports

  • Disadvantage

    Does not offer customer support via emails

  • Disadvantage

    Phone and chat support are not available on weekends

Intuit QuickBooks

Intuit QuickBooks

Multi-industry Solution

Geekflare rating score 4.5 out of 5
4.5
|
  • Grant Management
    Yes
  • Mobile App
    Yes
  • Customer Support
    Live Chat, Phone, Support Page

About Intuit QuickBooks

Intuit QuickBooks is an accounting software that enables nonprofit organizations to accept, monitor, and manage donations. It allows users to accept online donations from various donors and entities by credit card, debit card, bank transfer, cash, or check.

QuickBooks Enterprise plan lets users securely manage thousands of donors, vendors, and items. It also supports adding up to 40 users. QuickBooks was launched in 1998 in the USA and offers a mobile app for nonprofits to record money on mobile devices. The features of this software are explained in our QuickBooks Online Review.

Intuit QuickBooks Features

  • Key feature

    Categorize revenue expenditures by fund or program

  • Key feature

    Custom reports based on the data with organizational importance

  • Key feature

    Budget tracking by fund or program

  • Key feature

    Financial reporting and bank reconciliations

  • Key feature

    Grant and donor management

  • Key feature

    Connect to the bank to get instant updates for expense tracking and cash flow

  • Key feature

    Import transactions from apps like Fundly or DonorPerfect

  • Key feature

    Handles nonprofit management across the year to prepare organizations for tax filing

  • Key feature

    Instant report creation and automatic emailing for the stakeholders

  • Key feature

    Generate reports on statements of financial position, statements of financial activities, budget versus actual, etc.

Intuit QuickBooks Pros/Cons

  • Advantage

    Integration with 750+ apps

  • Advantage

    Supports financial planning with real-time data

  • Advantage

    Generate reports for annual IRS filing

  • Disadvantage

    Steep learning curve

  • Disadvantage

    Advanced bank reconciliation feature is unavailable

Intuit QuickBooks Pricing

The subscription plans of Intuit QuickBooks are explained below.

PlanPricing (monthly)Offerings
Plus$45Includes 5 users, Bill management, Multiple currencies, Invoice and payments, Tax deductions, Comprehensive reports
Advanced$100Includes 25 users, Powerful reports, Workflow automation, Data restoration, 24/7 support & training, Revenue Recognition
Desktop solution with hosting$180Built-in templates and statements, Online data backup and restore, Advanced Reporting, Dedicated account team, Online access to training, Add up to 40 users
Sage Intacct

Sage Intacct

Best for Complex Financials

Geekflare rating score 4.2 out of 5
4.2
|
  • Grant Management
    Yes
  • Mobile App
    Yes
  • Customer Support
    Support Center, Phone, Web Chat, Knowledgebase
Custom Pricing
Get Sage Intacct

About Sage Intacct

Sage Intacct is designed specifically for small to medium-sized nonprofits. It helps foundations, associations, faith-based and governmental organizations manage their finances, track donations, and generate reports. Thus, these organizations fully comply with regulations and remain transparent to their donors.

Sage nonprofit accounting software, founded in 1999, offers additional advanced features, including fund accounting, grant management, nonprofit revenue recognition, spend management, and multi-entity consolidations.

Sage Intacct Features

  • Key feature

    Manage grant, fund, project, and donor accounting

  • Key feature

    Track, report, and reimburse grants accurately

  • Key feature

    Automate accounts payable and spend management

  • Key feature

    Easy consolidation of multiple entities for local and global operations

  • Key feature

    Real-time data for budgeting, planning, and forecasting

  • Key feature

    Automate nonprofit workflows through fundraising, fixed asset management, and project management

  • Key feature

    Payroll and HR management with employee benefits, time and expenses, and employee performance monitoring

Sage Intacct Pros/Cons

  • Advantage

    24/7 access to financial, people, and operational data

  • Advantage

    Nonprofit revenue recognition

  • Advantage

    Role-based reports, dashboards, and data visualizations

  • Disadvantage

    24/7 phone support is not available for all users

  • Disadvantage

    Transparent pricing information is not available

Xero

Xero

Best for Cloud Collaboration and Reporting

Geekflare rating score 4.5 out of 5
4.5
|
  • Grant Management
    No
  • Mobile App
    Yes
  • Customer Support
    Email, Callback on Request, Support Center
$14.50/month
30-Day FREE Trial
Get Xero

About Xero

Xero is online accounting software for nonprofits and charities. It allows nonprofits to get an overview of their business and track its financial health. Xero is a good choice for nonprofits looking for a straightforward application for recurring pay runs.

Besides employee pay records, Xero securely stores employee data and personal details. It also creates and manages invoices, including unpaid and overdue invoices. Xero was launched in 2006 in New Zealand. Read more about Xero in our Xero Accounting Review.

Xero Features

  • Key feature

    Powerful dashboard to monitor in and out cashflow of non-profit

  • Key feature

    Cash summary report to make plans and track all organizational expenses

  • Key feature

    Keep basic pay records online and run payroll for limited nonprofit employees

  • Key feature

    Dedicated apps for use on phone or mobile devices

  • Key feature

    Create customized reports with different visualization styles

  • Key feature

    Apply formula to calculate and compare budget versus actuals

  • Key feature

    Bank reconciliation feature to review and match transactions

Xero Pros/Cons

  • Advantage

    Offers discount rate for non-profit organizations

  • Advantage

    Manage projects with task breakdown and budget estimate

  • Advantage

    Share financial reports with donors, volunteers, and other stakeholders

  • Disadvantage

    Invoice has limited customization feature

  • Disadvantage

    Email support team could respond faster

Xero Pricing

Xero subscription tiers are mentioned below.

PlanPricing (monthly)Offerings
Starter$14.5020 invoices, online quotes, bank account reconciliation
Standard$23Short-term cash flow, business snapshot
Premium$31Use multiple currencies
MoneyMinder

MoneyMinder

Good for Budgeting and Cash Flow

Geekflare rating score 4.8 out of 5
4.8
|
  • Grant Management
    No
  • Mobile App
    Yes
  • Customer Support
    Phone, Email, Live Chat

About MoneyMinder

MoneyMinder is a nonprofit treasurer accounting software with the necessary features and functionalities to operate a charitable agency swiftly. Volunteers with no prior bookkeeping experience can also use the tool so that nonprofits can save money on accountants and bookkeepers.

MoneyMinder has a Document Library module that stores receipts, forms, records, other documents, and tax filing templates. It helps users create a budget or forecast expenditure based on charitable activities and categories. MoneyMinder was established in 2003 in Washington, US.

MoneyMinder Features

  • Key feature

    A Bookkeeping module to manage banking registers, transactions, reconciliations, reports, and transfers

  • Key feature

    Track fundraising, reimbursements, and payments, and email them to the stakeholders

  • Key feature

    Prepare annual reports, perform audits, and calculate 990EZ totals

  • Key feature

    Integrate with bank accounts, Square, PayPal, Venmo, and Stripe

  • Key feature

    Accurate record of all money coming and going

  • Key feature

    Collect payment for an online store through a credit card or e-check

  • Key feature

    Treasureโ€™s report to collect necessary data for audits and tax forms

MoneyMinder Pros/Cons

  • Advantage

    Free, US-based chat, email, and phone support

  • Advantage

    Ad-free platform with no set-up fees

  • Advantage

    30-day free trial of Full Edition

  • Disadvantage

    Customer support is not available on weekdays and holidays

  • Disadvantage

    Users must subscribe to Full Edition for the whole year

MoneyMinder Pricing

MoneyMinder offers 2 straightforward plans, as mentioned below.

PlanPricingOfferings
Free Edition$0Custom budget, online payment collection, forecasting
Full Edition$199/yearBank reconciliations, one-click budget reports, contact statements
Zoho Books

Zoho Books

Best for Project Accounting and Expenses

Geekflare rating score 4.5 out of 5
4.5
|
  • Grant Management
    Yes
  • Mobile App
    Yes
  • Customer Support
    Email, Phone, Chat

About Zoho Books

Zoho Books is a well-rounded not-for-profit accounting software for any nonprofit agency. Whether it’s a new charitable foundation or a nonprofit with global operations, it offers scalable features and pricing models to fit the needs of every organization devoted to a good cause.

Organizations can focus on grants, donations, and events while the application swiftly manages all the inflow of donation funds and categorizes them. Zoho was established in 1996.

Zoho Books Features

  • Key feature

    Set up a nonprofit organization quickly and easily

  • Key feature

    Dashboard showcasing projects, expenses, and cash flow

  • Key feature

    Create separate expense accounts for fund categorizing and reporting

  • Key feature

    Accept donations in multiple currencies

  • Key feature

    Record payments and send payment receipts to the donors via email

  • Key feature

    Generate reports to assess progress and get insights into the advancement

  • Key feature

    Track multiple projects, monitor employee costs, and generate reports

Zoho Books Pros/Cons

  • Advantage

    14-day free trial for all plans

  • Advantage

    Free support via email, phone, and chat

  • Advantage

    Android and iOS mobile apps

  • Disadvantage

    Free plan does not support add-ons

  • Disadvantage

    Does not offer software for Mac devices

Zoho Books Pricing

The 6 subscription plans of Zoho Books are elaborated below.

PlanPricing (monthly)Offerings
Free$0Create invoices, send quotes, automatic payment reminder
Standard$15Setup recurring expenses,  transaction period locking, connect bank feeds
Professional$40Manage vendor bills and payments, manage retainers, record multi-currency transactions
Premium$60Budgeting, cash flow forecasting, managing custom functions
Elite$120Warehouse management, shipment tracking, composite items
Ultimate$240Custom dashboard, data visualization, collaborative report creation
Aplos

Aplos

Good to Manage Donors and Funds

Geekflare rating score 4.6 out of 5
4.6
|
  • Grant Management
    Yes
  • Mobile App
    No
  • Customer Support
    Email, Phone, Support & Training Center
$59.25/month
15-Day FREE Trial
Get Aplos

About Aplos

Aplos is an advanced fund accounting platform for churches to manage finance, donations, and people. Over 40,000 charitable foundations use this tool to keep their tax-exempt status undamaged. It allows all sizes of nonprofit groups and faith-based organizations to run their operations, manage their business, and actively engage with their communities and donors.

Aplos is also renowned for nonprofit bookkeeping services. Users can request on-demand services to process challenging accounts or tax returns. Its bookkeeping team offers accurate records, better financial statements, and simplified solutions. Aplos was founded in 2009.

Aplos Features

  • Key feature

    Flexible chart of accounts with fund tracking and tags

  • Key feature

    Easily track funds, grants, and special programs for the financial reporting requirements

  • Key feature

    Create personalized financial reports for departments, campaigns, and projects

  • Key feature

    One-click standard nonprofit report generation, including fund income statement

  • Key feature

    Identify tax-deductible income by purpose and track other incomes

  • Key feature

    Manage membership and sponsorship invoices

  • Key feature

    Budget charitable activities by tags or funds

  • Key feature

    Fixed asset tracking and expense and income allocations

Aplos Pros/Cons

  • Advantage

    Generate financial statements and reports on budgeting and donation

  • Advantage

    15-day free trial for all subscription plans

  • Advantage

    Form 990 reports and donor CRM database

  • Disadvantage

    24/7 phone support is not available

  • Disadvantage

    Steep learning curve

Aplos Pricing

Aplos has 3 pricing tiers, as mentioned below.

PlanPricing (monthly)Offerings
Lite$59.25Fund accounting, donation tracking, contribution statements
Core$74.25Budgeting, recurring transactions, pledge tracking
Advanced$189Budgeting by fund, income & expense allocations, fixed asset tracking
Accounting Seed

Accounting Seed

Best for Salesforce Integration

Geekflare rating score 4.2 out of 5
4.2
|
  • Grant Management
    Yes
  • Mobile App
    No
  • Customer Support
    Email, Support Center
Custom Pricing
Get Accounting Seed

About Accounting Seed

Accounting Seed is easy to operate and manages a wide range of nonprofit tasks and campaigns for churches and other charitable organizations. Organizations can even train their volunteers to use the tool to save money on additional staff hiring.

Accounting Seed offers a full grip and oversight over the financial management lifecycle of a charitable agency. It enables one to view financial statements, donation reports, and tax filing in real-time. Thus, organizations can quickly deal with donors and granting authorities to secure more donations for their charitable cause.

Accounting Seed was launched in 2011 and currently serves over 1,000 customers and more than 50,000 users worldwide.

Accounting Seed Features

  • Key feature

    Automatically record donations received on Salesforce

  • Key feature

    Track restricted, unrestricted, and temporarily restricted donations

  • Key feature

    Fund accounting in multiple currencies

  • Key feature

    Manage multiple fundraising campaigns, grants, and donors

  • Key feature

    Single platform to manage accounting and CRM

  • Key feature

    Real-time business performance view with affordable integrations

  • Key feature

    Manage more than one charitable agency in one centralized tool

  • Key feature

    No-code reporting on impactful campaigns and profitable fundraising events

  • Key feature

    Analyze program and other expenditures

Accounting Seed Pros/Cons

  • Advantage

    In-app AI assistance to provide answers, task lists, and walk-throughs

  • Advantage

    Detailed API instruction and documentation

  • Advantage

    Easily connects with Salesforce cloud applications

  • Disadvantage

    Transparent pricing is not available

  • Disadvantage

    Does not offer a mobile app

Akaunting

Akaunting

Open-Source Accounting Software

Geekflare rating score 4.0 out of 5
4.0
|
  • Grant Management
    No
  • Mobile App
    Yes
  • Customer Support
    Forum, Ticket Submission

About Akaunting

Akaunting is a popular accounting tool for small nonprofit agencies. It helps them cut costs while complying with stringent charitable foundation policies. It also makes online finance management easy with accounting, expense tracking, and other features.

The self-hosted, on-premise version of this open-source software is available for free. Akaunting was launched in 2017. Over 200,000 users use this tool in 100+ countries.

Akaunting Features

  • Key feature

    Dashboard for all accounts

  • Key feature

    Track bills and expenses

  • Key feature

    Multiple currencies and recurring payment reminders

  • Key feature

    Banking services and reconciliations

  • Key feature

    Custom reports for tax fillings like Form 990

  • Key feature

    Easily send professional-looking invoice

  • Key feature

    Create incomes, expenses, and items categories

  • Key feature

    Simple automation to manage multiple tasks and clients

  • Key feature

    Maintain clear records for regulations or compliance requirements

Akaunting Pros/Cons

  • Advantage

    Translates in 50+ languages

  • Advantage

    Client portal to share invoices and transactions

  • Advantage

    App store with 50+ apps

  • Disadvantage

    Dedicated support is not available for free

  • Disadvantage

    No app is available in on-premise plans.

Akaunting Pricing

Akaunting has 7 subscription plans, as listed below.

PlanPricingOfferings
Standard on-premise$01 company, 1 user+1 accountant, 1,000 invoices
Premium on-premise$72/year10 companies, unlimited vendors, unlimited reports
Elite on-premise$168/yearRecurring payment reminders, multiple currencies, manage employees
Ultimate on-premise$684/yearMultiple bank accounts, import bank transactions, list products or services
Premium Cloud$24/monthDouble entry, bank feeds, expense claims
Elite Cloud$56/monthProjects, payroll, receipt scanning
Ultimate Cloud$145/monthBudgeting, custom fields, auto-schedule reports
Cougar Mountain

Cougar Mountain

Best for Digitizing Offline Accounts

Geekflare rating score 3.8 out of 5
3.8
|
  • Grant Management
    Yes
  • Mobile App
    No
  • Customer Support
    Email, Phone, Online Forum
Custom Pricing
Demo Available
Get Cougar Mountain

About Cougar Mountain

Denali Fund from Cougar Mountain is designed as a bespoke solution for non-profit organizations that are trying to stay on top of their fund accounting. In addition to revenue and expenses, it shows EBITA (Earnings before interest, taxes, and amortization) and cash on hand so the organizations can make data-driven decisions.

Cougar Mountain software was launched in 1982 and serves nonprofits and small and mid-sized businesses.

Cougar Mountain Features

  • Key feature

    Get transparency in federal grants, private grants, and corporate sponsorships

  • Key feature

    Fund tracking and accounting without any gap

  • Key feature

    Create customized reports according to organizational needs

  • Key feature

    Audit trail and flexibility in reporting

  • Key feature

    Seamless onboarding with guidance through installation, setup, and training

Cougar Mountain Pros/Cons

  • Advantage

    Easy-to-use interface with smooth navigation

  • Advantage

    Comprehensive GAAP and FASB compliance

  • Advantage

    Track of all encumbrances in the non-profit

  • Disadvantage

    Does not offer live chat support

  • Disadvantage

    Minimum 8 hours of training is required to run the tool

Nonprofit Accounting Software Comparison Table

The following table provides a comparative summary of pricing and key features of the best nonprofit accounting software.

Nonprofit Accounting Software
Pricing (monthly)
Integration Support
Bank Reconciliation
Explore
Wave Accounting

Wave Accounting

4.2
/5
FREE
Integration through Zapier
Yes
MIP Fund Accounting

MIP Fund Accounting

4.0
/5
Pricing on request
No
Yes
Intuit QuickBooks

Intuit QuickBooks

4.5
/5
$45
Fundly, DonorPerfect
Yes
Sage Intacct

Sage Intacct

4.2
/5
Pricing on request
Stripe, PayPal
Yes
Xero

Xero

4.5
/5
$14.50
Payroll apps
Yes
MoneyMinder

MoneyMinder

4.8
/5
FREE
Stripe, Square, PayPal, Venmo and more
Yes
Zoho Books

Zoho Books

4.5
/5
FREE
Stripe, PayPal, Payoneer, Square
Yes
Aplos

Aplos

4.6
/5
$59.25
Partner integration
No
Accounting Seed

Accounting Seed

4.2
/5
Pricing on request
Salesforce
Yes
Akaunting

Akaunting

4.0
/5
FREE
2Checkout, PayPal Express, PayPal Sync, Square
No
Cougar Mountain

Cougar Mountain

3.8
/5
Pricing on request
No
No

What Is Nonprofit Accounting Software?

Any tool that helps manage accounting tasks for a nonprofit organization is known as accounting software for nonprofits. However, there is a fine line between accounting for for-profit and nonprofit organizations. Business accounting mainly tracks profit and loss. It follows how much the for-profit organization spends, earns, saves, or loses.

On the contrary, nonprofit accounting is all about fund accounting. The tool needs to monitor the fundโ€™s flows, such as where the money is coming from and where it is going. Also, the tool processes all incoming donations and keeps the donors and board members updated on how the organization uses donations.    

Why Does a Nonprofit Organization Need an Accounting Software?

A nonprofit organization requires the right accounting tool to keep its nonprofit, tax-exempt, and tax claim back statuses active. To keep these statuses intact, all nonprofit organizations must process some accounting tasks. Find below some common reasons to use accounting software for nonprofits:

  • Nonprofits must meet stringent financial accounting standards, such as FAS 116 or FAS 117, and need a nonprofit accounting tool.
  • Buddying charitable organizations have limited volunteers and staff. Hence, they need an automatic tool that is easy to learn.
  • Such devices also help with additional accounting tasks, such as tracking grants, meeting reporting requirements, producing balance sheet reports, updating donors on donation utilization, and more.
  • These tools format accounting reports for the Return of Organization Exempt from Income Tax or Form 990.      

The Benefits of Nonprofit Accounting Software

Both global nonprofit organizations and local charitable entities need a powerful accounting tool to carry out nonprofit accounting for the following benefits: 

  • Accept donations online or offline transparently
  • Become eligible for large donations or grant requirements by reporting and planning
  • Generate reports on the inflow and outflow of money for the stakeholders, donors, and board members
  • Cloud-based accounting software that saves users from setting up costly IT infrastructure to install standalone apps
  • Helps to reclaim tax return filling and comply with HMRC and IRS requirements
  • Automate various recurring tasks and reduce human error.

Final Words

Nonprofit accounting software is beneficial for nonprofit organizations, as it allows them to manage resources. These tools also help file proper tax returns, keeping the organizationโ€™s nonprofit status intact.

Use any of the above accounting tools for nonprofit organizations and comply with local and international laws for nonprofit entities. 

Explore more Accounting Solutions