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Top Rated Nonprofit Accounting Software with Billing & Invoicing in 2026

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Verified reviewer profile picture

All user reviews are verified by in-house moderators and provider data by our software research team.  Learn more

Last updated: February 2026

Billing and invoicing streamline the financial processes by automating invoice generation, tracking payments, and linking transactions to CRM records. This efficiency allows nonprofits to focus more on their mission-driven work. Our reviewers in nonprofit accounting software rated this feature as important.

3 Best Nonprofit Accounting Software with Billing & Invoicing

  • QuickBooks Enterprise
  • QuickBooks Online Advanced
  • QuickBooks Online - Highest rated for billing & invoicing

See other top Nonprofit Accounting products with billing & invoicing

How we picked the 3 top rated products

We chose the high-performing solutions on this list based on verified user ratings on our site. Depending on available data, qualifying products either had to be among the most user-reviewed or the most searched-for products in the nonprofit accounting software category. They also needed to have sufficient reviews about billing & invoicing, have a minimum user rating of 3 out of 5 for that feature, and show evidence of U.S. market presence. We then added a distinction for the product with the highest rating for billing & invoicing based on our proprietary ratings and reviews. Sponsorship or client status has no influence on the selection of these products, but it may impact the order in which products appear.

Details for the 3 best products

QuickBooks Enterprise logo

QuickBooks Enterprise

4.5
(20.5K)
visit website

User insights about the billing & invoicing feature

Reviewers appreciate QuickBooks Enterprise's billing and invoicing capabilities for their ease of use and efficiency. They find it simple to create, customize, and send invoices, and value the automation of recurring invoices. Users highlight the integration with other financial tools and the ability to track outstanding invoices and payments. They also mention the customizable templates and the seamless integration with inventory management. However, some users note difficulties with accepting payments on multiple accounts and limited integration with Outlook.
“Makes our system much easier to track billing and invoicing. Allows us to quickly make modifications and close the invoices when payment is received. The reports are very useful reminders.”
RW

Randy W.

IT Manager

“QuickBooks Enterprise provides a flexible billing and invoicing system with options to tailor pricing and features according to business needs, which is beneficial for scaling”
LG

Lorenzo G.

Financial analyst

Nonprofit Accounting key features coverage

QuickBooks Enterprise offers 5 out of the 5 key features for Nonprofit Accounting software identified by reviewers:

Accounting4.6
General Ledger4.5
Financial Reporting4.6
Income & Balance Sheet4.6
Bank Reconciliation4.5

Pros and cons based on 20,593 verified reviews

61% of users rated QuickBooks Enterprise 5 out of 5 stars, while 2% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 20,593 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Comprehensive expense tracking

Ideal for small businesses

Effective financial management

Streamlined bookkeeping

Efficient tax management

Cons:

Frequent issue resolution challenges

Slow performance speed

Disruptive software updates

High cost concerns

Unreliable customer service

See pros and cons details

Pricing

Starting price:$2210 flat rate/per year|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

QuickBooks Online Advanced logo
4.4
(1K)

User insights about the billing & invoicing feature

Reviewers indicate that QuickBooks Online Advanced automates the billing and invoicing process, saving time and reducing errors. They appreciate the ease of creating and sending invoices, as well as the ability to customize invoice templates. Users find the integration with QBO payments convenient and value the detailed reporting options. However, some users mention that setting up invoice formats can be time-consuming and that the customization options are not as extensive as in the desktop version.
“Billing and invoicing in QuickBooks is both easy and very intuitive. We create invoices for our clients daily and are able to both customize the way they look and streamline the process. I especially appreciate the ability to directly email the invoices to our clients from QuickBooks.”
ED

Eugene D.

Project Manager

“The way to write up an invoice & send it is very user friendly! My only complaint is that the set up for customizing invoices & estimates is not as in depth / customizable as the version on QB Desktop App.”
JW

Julia W.

Office Manager

Nonprofit Accounting key features coverage

QuickBooks Online Advanced offers 5 out of the 5 key features for Nonprofit Accounting software identified by reviewers:

Accounting4.6
General Ledger4.4
Financial Reporting4.5
Income & Balance Sheet4.6
Bank Reconciliation4.5

Pros and cons based on 1,035 verified reviews

60% of users rated QuickBooks Online Advanced 5 out of 5 stars, while 4% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 1,035 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Convenient remote access

Efficient bookkeeping

Comprehensive tracking features

Robust financial management

Organized multi-entity management

Cons:

Challenging issue resolution

Limited desktop version compatibility

High costs and confusing pricing

Inconsistent customer service

Subpar mobile accessibility

See pros and cons details

Pricing

Starting price:$235 flat rate/per month|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

QuickBooks Online logo
4.3
(8.3K)

User insights about the billing & invoicing feature

Users find QuickBooks Online's billing and invoicing capabilities easy to use and efficient. They appreciate the ability to create, customize, and send professional-looking invoices quickly. Reviewers highlight the automation of recurring invoices and payment reminders, which saves time and reduces errors. They also value the integration with other management software and the ability to track payments and outstanding invoices. However, some users mention limitations in customization options and occasional issues with invoice duplication.
“I use QuickBooks Online more so for billing/invoicing over expense tracking so the ability to get that task done takes priority over all others. I have found the process to be easy for me to disseminate invoices and for my customers to receive them and remit payment online. ”
MS

Michelle S.

Small Business Owner/Brand Designer

“QuickBooks Online makes billing and invoicing a breeze. Users can create professional-looking invoices, set up recurring invoices, and accept online payments.”
MG

Massimiliano G.

Graphic Designer

Nonprofit Accounting key features coverage

QuickBooks Online offers 5 out of the 5 key features for Nonprofit Accounting software identified by reviewers:

Accounting4.5
General Ledger4.4
Financial Reporting4.4
Income & Balance Sheet4.5
Bank Reconciliation4.4

Pros and cons based on 8,328 verified reviews

57% of users rated QuickBooks Online 5 out of 5 stars, while 5% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 8,328 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Cloud-based accessibility

Ideal for small businesses

Seamless integrations

Comprehensive accounting features

Efficient tax management

Cons:

Frequent bugs and crashes

Limited desktop features

Recurring costs and price increases

Inadequate customer support

Complicated transaction management

See pros and cons details

Pricing

Starting price:$38 flat rate/per month|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

Other Top Rated Nonprofit Accounting Software with Billing & Invoicing in 2026

Blackbaud Financial Edge NXT logo

Blackbaud Financial Edge NXT

Cloud fund accounting software for social good organizations

visit website
Financial Edge NXT delivers comprehensive fund accounting tools that allow organizations to streamline financial processes and demonstrate accountability

Read more about Blackbaud Financial Edge NXT

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Fund EZ logo

Fund EZ

Accounting Software Built for Your Nonprofit

visit website
Empower your nonprofit with Fund EZ! Effortlessly create and track budgets for diverse funds, programs, projects, grants, funding sources, and departments. Achieve financial excellence with Fund EZ's all-in-one solution!

Read more about Fund EZ

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Aplos logo

Aplos

Category Leaders

Aplos: where every dollar finds its purpose

visit website
Aplos provides the robust accounting framework necessary to track restricted vs unrestricted funds and generate comprehensive, auditor-friendly reports. Our features are crafted to aid budgeting, automate complex allocations, and provide real-time insights into your financial health.

Read more about Aplos

Users also considered
Sage Intacct logo

Sage Intacct

Category Leaders

Best-in-class Cloud ERP for Finance

visit website
The #1 Nonprofit Cloud Accounting and Financial Management System Powering Mission-Driven Nonprofits. The AICPA’s preferred provider.

Read more about Sage Intacct

Users also considered
MIP Accounting logo

MIP Accounting

Fund accounting for government organizations and nonprofits

visit website
MIP Fund Accounting is a comprehensive, configurable fund accounting solution designed to meet and handle the complex financial management and fund accounting needs of nonprofit and government organizations.

Read more about MIP Accounting

Users also considered
QuickBooks Enterprise logo
Category Leaders

Enterprise accounting, FSM and inventory management solution

QuickBooks Desktop Enterprise is an accounting software for small businesses which provides users with real-time access to customer, employee, and vendor information. The software includes tools for managing inventory, shipping, sales orders, pricing, tasks, invoicing, reporting, and more.

Read more about QuickBooks Enterprise

Users also considered
QuickBooks Online logo
Category Leaders

Accounting and business management software

QuickBooks Online is an all-in-one online business software designed to help manage business finances. The platform is built to scale businesses, unlocking insights and providing the functionality of a larger team, all on one integrated platform.

Read more about QuickBooks Online

Users also considered
QuickBooks Online Advanced logo
Category Leaders

Accounting & business management for small businesses

QuickBooks Online Advanced is a web-based accounting & business management solution which enables small businesses to track sales, inventory, financial accounts & payroll from a single dashboard

Read more about QuickBooks Online Advanced

Users also considered
NetSuite logo
Category Leaders

AI-powered cloud-based business management suite

NetSuite's ERP provides one integrated, cloud solution to manage your entire organization and accelerate your mission. Gain efficiencies with a powerful nonprofit fiscal management system built to meet the unique needs of your nonprofit.

Read more about NetSuite

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Sage Accounting logo

Accounting software for small businesses

Sage Accounting is an accounting system for small business owners. It has features to help users forecast their cashflow, send and track invoices and act on real-time reporting. Users can manage their business from anywhere, at any time, from the cloud and with mobile functionality. Sage Accounting application is available for iOS and Android.

Read more about Sage Accounting

Users also considered
MoneyMinder logo
Category Leaders

Simple accounting software for volunteers.

Simple nonprofit accounting software for volunteer-based groups (PTAs, PTOs, Booster Clubs, Sports Teams, Scouts, Service Clubs, etc.)

Read more about MoneyMinder

Users also considered
MonkeyPod logo

Your all-in-one nonprofit management platform

MonkeyPod is an all-in-one platform to manage nonprofit accounting, donor management, grants management, CRM, email marketing, online fundraising, and more. Add unlimited users, CRM entities, email subscribers, online fundraising pages, pipelines, and more at no additional cost.

Read more about MonkeyPod

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Kashoo logo

Online accounting software for small businesses

Kashoo is simple cloud accounting for small business owners who want the control and simplicity of doing their own books. It provides small business owners with the ability to run their business the way they want to, with tools for invoice management, payment processing, reporting, and more.

Read more about Kashoo

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ZipBooks logo

Accounting and online invoicing software

ZipBooks is a cloud-based accounting software that caters to the bookkeeping and accounting needs of small to medium-sized businesses and bookkeeping firms. The solution offers core accounting, financial reporting, online invoicing, expense tracking, credit card processing, and more.

Read more about ZipBooks

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OneStream logo

Corporate performance management solution for enterprises

OneStream is a unified corporate performance management (CPM) solution which enables businesses to manage their financial reporting, budgeting & forecasting

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Multiview ERP logo

Enterprise resource planning (ERP) solution

Multiview is a highly-scalable modular ERP software for scaling organizations which require more automation, control and insight into their operations. A fully-integrated suite of financials ranges from core accounting, budgeting and forecasting to materials management and workflow approvals.

Read more about Multiview ERP

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iplicit logo

Cloud-based accounting and financial management software

iplicit is a cloud-based software designed for businesses of all sizes that helps streamline accounting processes, generate business reports, and analyze financial datasets on a unified platform. Key features include summary charts, multi-currency, and purchase orders.

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MYOB Business logo

Online accounting & payroll for every business

Small Business cloud based accounting software to automate payroll, manage financial performance, tax and all your accounting needs.

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AccountsIQ logo

Cloud-based accounting software for medium-sized businesses

AccountsIQ is cloud-based accounting software that assists businesses in construction, retail, hospitality, and other sectors with cash flow forecasting, budgeting, and financial reporting.

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Denali Fund logo

Nonprofit accounting software

Denali FUND by Cougar Mountain Software is a cloud-based and on-premise accounting software designed specifically to help nonprofit organizations streamline & manage all accounting processes, including accounts payable & receivable, general ledger, bank reconciliation, payroll, and more

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AccuFund Accounting Suite logo

Online and Onsite Accounting Software for Nonprofits & Govt

AccuFund’s complete nonprofit financial management system improves all critical aspects of your nonprofit, from budget development to grants management to payroll and HR and accounts payable, selecting the modules that your nonprofit needs now and add others in the future as needs evolve.

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Approveit logo

Automate approval workflows across your entire company!

Approveit automates approval workflows right in Slack or Email. Integrations with XERO, QuickBooks, Freshbooks, Jira, and over 3000 apps through Zapier help to avoid routine manual tasks. Submit and approve requests anytime, in one place!

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Clay logo

Software contable y financiero en Chile

Clay es el software contable y financiero en la Chile que conecta a contadores y dueños de negocio en un mismo lugar. Es el punto de encuentro donde ambos pueden trabajar con la misma información, siempre actualizada y respaldada desde sus fuentes de verdad: 14 bancos, SII y TGR.

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Infor SunSystems logo

Financial management software that can adapt to any market

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Xledger logo

Empower ambition with Xledger.

Xledger is a true-cloud financial software that serves over 18,000 customers worldwide. For over 20 years, Xledger has been a leader in automated accounting software and has been empowering ambitious companies around the globe.

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Key features for Nonprofit Accounting software

Based on GetApp's analysis of verified user reviews collected between July 2021 and August 2024.

  • Accounting: Reviewers value detailed record-keeping, the ability to track income and expenses, integration with CRM and donation platforms, and user-friendly design for non-accountants. 100% of reviewers rated this feature as important or highly important.
  • General Ledger: Users appreciate tracking income and expenses, customizable charts of accounts, drill-down options, and the ability to generate detailed and accurate financial reports. 99% of reviewers rated this feature as important or highly important.
  • Financial Reporting: Reviewers highlight customizable reports, easy sharing with boards, up-to-date financial insights, and the ability to monitor and communicate financial health effectively. 98% of reviewers rated this feature as important or highly important.
  • Income & Balance Sheet: Users value the ability to track financial standings, customize reports, identify discrepancies easily, and provide transparent financial overviews for stakeholders. 97% of reviewers rated this feature as important or highly important.
  • Bank Reconciliation: Reviewers appreciate the ease of linking bank accounts, automated reconciliation processes, clear delineation of cleared/uncleared items, and the time-saving features. 95% of reviewers rated this feature as important or highly important.