Top 10 Online Payment & Billing Solutions for Nonprofits & Charities: Get Paid Faster to Keep Your Organization Funded and More


As a nonprofit, the last thing you need to worry about (again) is money—getting paid isn’t easy for anyone, but in your business, it can prove to be even more of a challenge. Fortunately, there are tools out there to help you get more out of your billing and payments, no matter what type of charity or nonprofit organization you operate. 

You need a quick, easy way to manage your finances and billing, accept donations and vendor payments, create reports, and more. While traditional accounting software does some of this, the newer platforms that are available will make sure that you get all of the solutions that you need. You can find tools that will assist with everything that nonprofits are missing:

  • Easy online billing and payments
  • Automated reminders and recurring billing and donation tools
  • Donor and campaign management 
  • Easy invoicing and customization
  • Scalable platforms that are based in the cloud
  • And more!

What features does your organization need to make sure that you’re getting paid? How much more time could you spend on cultivating donors or other efforts in your organization if you weren’t trying to collect on all those invoices or track down those donors? With the tools on the list below, you’re sure to save a small fortune in time, effort, and money that’s not being wasted on endless hours of billing. 

We’ve taken the time to review the top 10 tools for billing and payments for nonprofit organizations, making sure to cover some that are specifically for nonprofits and some that are just the best tools available today for any industry. (And, if you reach out, we’ll cover all the ways that the virtual receptionists at can help you get paid and take care of your donors with overflow calling, outbound calling, live chat, and more.)

1. Invoicely

Invoicely logo

Invoicely is our first pick because it’s one of the few options that offers a free solution for basic billing, invoicing, and payments. It even comes with apps for iOS and Android and can be used by solo users and teams alike, making it perfect for nonprofits of any size. It can be used to streamline plenty of tasks by automating workflows, organizing billing, and tracking expenses, payroll, and more. 

Invoicely can be integrated with hundreds of different tools and apps that are available today, including several payment processors and CRMs. You can even access mobile invoicing, custom invoice templates that can be branded for your organization, and more. Plus, you can track it all with custom labels and a customizable dashboard that can be scaled to your needs. 

  • Free option? Yes
  • Price: Paid plans start at $10 per month
  • Rich client information database
  • Free forever basic option
  • Robust reporting
  • Workflow automation and AI
  • Automated payments and reminders
  • Custom invoicing

2. Intuit QuickBooks

Intuit Quickbooks logo

Intuit QuickBooks is one of the oldest options for accounting software, but that doesn’t mean that it’s outdated. In fact, Intuit has done a great job at keeping up with the ever-changing needs of today’s professional world, including for nonprofits and charitable organizations. This tool integrates with thousands of other software suites and apps and can handle billing, accounting, and all kinds of needs. 

QuickBooks is cloud-deployed so it can be scaled to fit the exact needs of your business. It can be customized to manage your expenses, vendors, and even handle your donations and bookkeeping so that everything is streamlined and in the same place. It also has receipt capture, tax tools, and mobile apps available. 

  • Free option? No, but there is a trial
  • Price: Starts at $15 per month
  • Mobile tools
  • Customizable invoices
  • Handle payroll and taxes
  • Receipt capture feature
  • Integrates with hundreds of apps

3. Zoho Invoice

Zoho Invoice logo

Zoho Invoice offers all of the invoicing tools that you need, and it’s free for solo users so smaller nonprofits and charities can find a lot of value here. The Zoho family includes several products for business management and this Invoice solution is just one of them. It will allow you to convert estimates to invoices with a few clicks and automate much of your billing-related work.

Zoho Invoice also includes a convenient customer portal for online payments and it accepts multiple currencies and can be used in multiple languages. You can even track hours and unbilled expenses so that you have everything organized for yearly reporting, grant writing, and more. 

  • Free option? Free for single users
  • Price: Plans start at $9 per month 
  • Automated reminders and payments
  • Branding and customization
  • Online payment portal
  • Multiple languages and currencies
  • Estimate-to-invoice conversion

4. FreshBooks

FreshBooks logo

For a fresh look at keeping books, FreshBooks claims to have everything that you need. We like this platform for its simplicity while still having a robust selection of features, and appreciate that it offers a retainer feature, time tracking tools, and the handy estimate-to-invoice conversion option so that billing is a breeze. 

FreshBooks can be customized and scaled to your needs and apps are available for your iOS and Android devices. Users on iOS will love the mileage tracking feature that’s built in and double-entry accounting makes sure that your records are well-kept. You’ll be able to customize the dashboard and get easy access to reports, too. 

  • Free option? No
  • Price: Starts at $15 per month
  • Hundreds of integrations
  • Fee-based payment gateway
  • Retainer feature
  • Mobile apps available

5. Invoice2Go

Invoice2Go logo

Invoice2Go offers one of the simplest cloud-based invoicing and payment solutions available today. It's a great choice for nonprofits and charities on a budget, and it still offers plenty of features for your money. It even comes with a money-back guarantee and there are never setup fees or contracts to worry about. 

This app makes it easy to create invoices on the go and make sure that you get paid on time. You can accept all kinds of payment methods and even send invoices that include a “pay now” button to get paid instantly. There are even apps available for iOS and Android and the customizable dashboard includes detailed reporting. 

  • Free option? No
  • Price: $3 per month to start
  • Robust reporting
  • Lead generation tools
  • Custom invoices and templates
  • Track billable and unbilled hours
  • Accept online payments easily

6. Aplos

Aplos logo

Aplos is a dedicated accounting tool designed specifically for nonprofit organizations. It has plenty of funding-based accounting features and donor tools, as well as a general ledger that’s designed specifically for nonprofits. The software includes event registration, campaign management tools, and plenty of discounts that make it easy for new members to afford to get started. 

With Aplos, you can offer members and volunteers their own custom portals and you will find plenty of invoicing tools so that you can get paid easily. It’s a bit more expensive than many of the tools on this list, but the dedicated nonprofit features make it worth the money for most. Bear in mind that you will have to pay extra for expense tracking and tax tools, as well as premium reports. 

  • Free option? No, but discounts are available
  • Price: Starts at $59 per month
  • Donor management database
  • Automated donation receipts and reminders
  • Portals for specific audiences
  • Customizable websites included
  • Nonprofit-focused ledger

7. Nonprofit Plus

Nonprofit Plus logo

Nonprofit Plus is another dedicated nonprofit accounting suite that includes all of the tools that you need for payments and billing, as well as donor management, fund accounting, grant management, and even restricted funds accounting and management. The software offers customizable features and tools and an enhanced audit feature that follows the cash flow everywhere it goes. 

With Nonprofit Plus, organizations will have access to a platform that can be scaled to meet the needs of their specific billing and payment demands, including automated reminders, recurring donations and billing, and other features to encourage better accounting all around. 

  • Free option? No
  • Price: Quote-based
  • Inventory and donor management
  • Time tracking and billable hours
  • Easy payment portals
  • Customizable invoices
  • Reporting tools

8. Wave Accounting

Wave logo

Wave Accounting offers a convenient option for those on a tight budget. It has several features included free of charge, such as invoice templates galore, and you can even use the majority of the paid features on a pay-as-you-go basis. You can automate tasks and enjoy recurring billing, and even generate professional-looking invoices in seconds complete with all of your organization’s information. 

Wave Accounting also comes with monthly use features like its payroll management tools. There are customizable payment solutions and the app also includes an open API to integrate with all of the tools you already use. With the scalable cloud deployment, this platform offers it all and the prices are quite impressive. 

  • Free option? Yes, some features are free
  • Price: Paid plans start at $20 per month
  • Automated payments
  • Pay-per-use features
  • Recurring billing
  • Payroll and expense tracking
  • Client and donor data management

9. FreeAgent

FreeAgent logo

FreeAgent makes billing and invoicing easy, even for nonprofits with unique billing needs. The customizable features add up quickly and there’s a user-friendly dashboard that will keep you abreast of all of your billing and payment needs. The app is ideal for small to mid-size organizations that need an affordable solution and it includes a trial for those who want to test it before committing. 

FreeAgent offers Android and iOS apps and never has any setup fees or contracts. User support is readily available for those who need it and there is one of the most impressive databases of invoice templates available today in this software. When you need something simple that doesn’t skimp, this tool gets the job done and more. 

  • Free option? No, but there is a trial 
  • Price: $12 per month to start
  • Automated and recurring billing
  • A HUGE database of invoice templates
  • Seamless integrations
  • Workflow automations
  • Client database
  • Detailed reporting

10. OneUp

OneUp logo

The OneUp platform offers a new way to handle business banking, with a custom personal assistant that will take care of all of your billing, invoicing, and payment needs. It can even handle quotes, cash flow management, taxes, and more. You can use the digital document feature to scan and pay bills and even split payments. Plus, you can customize the platform for the unique needs of your nonprofit. 

With OneUp, you will find apps for iOS and Android, along with tools that can assist with other areas of managing your business. There are plenty of AI and automation features that you can capitalize on, as well, and Customer 360 views make it easy to track customers, donors, and more. 

  • Free option? No
  • Price: starts at $9 a month
  • Automated reminders
  • Digital accounting in minutes
  • Customer 360 views
  • Open API for easy integrations
  • Payment processing available
  • Premium security features

Take your billing and payments to the cloud and take along for even more efficiency

When you’re looking to improve your billing, invoicing, and payments, the tools available today should make that a fairly simple task. The programs listed above clearly offer a wide variety of solutions and tools to get the job done. Plus, you can take your efficiency one step further and enlist the assistance of the virtual receptionists at to field donor calls and queries, handle online billing questions, or take care of anything else that you need. 

You no longer have to hire a full team to handle your billing and accounting, or even rely on the single human that handles everything at the moment. With the modern billing and payment systems available today, anyone can manage billing with just a few clicks and everyone can appreciate that your organization is getting its money easier than ever before. 

To learn how the services of our virtual receptionists can help you further your billing and payment solutions, schedule a Live Chat consultation now. You’ll find out about our 24/7 customer service, which includes lead qualification, answering services, intake and scheduling, and more. We can even handle donation and payment collection by integrating with your credit card processing software and make outbound calls to track down those donors when they’re not following through. You can also email us or call (650) 727-6484.

Apps and Software
Written by Sean Lund-Brown

Sean Lund-Brown is a current Marketing Assistant for A graduate from Metropolitan State University of Denver, Sean graduated with a BA in Music and an individualized degree in Teaching Vocal Pedagogy.

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