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10 Best Billing Software for Agencies (2024)

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Updated on:
February 2, 2024
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Any agency aiming for success in 2024 and beyond needs reliable billing software. However, there’s more to billing software than meets the eye. Of course, it can send out invoices and let you watch the money roll in. But it also helps you juggle numbers, keep clients happy, and makes being an accountant easier.

Here are the top 10 billing software that can do all this and more.

What Is an Agency Billing Software?

Agency accountants have to juggle invoices, time sheets, and payment reminders. Historically, all this had to be done by hand, with books, ledgers, and a keen eye. While billing software doesn't replace the need for careful attention to detail, it does make everything more streamlined and less error-prone.

Every agency project is different, and time is always of the essence. For that reason, billing software that suits an agency must track the hours the team puts into projects, make detailed invoices that don't miss anything, and quickly handle payments.

While billing software is primarily about charging clients and getting paid, it includes many other related features. For example, it can analyze your financial data to give you insights that help you steer the agency to more profitable projects. It shows you where you're making great profits and where you might be lagging behind.

What Are the Benefits of Using a Billing System With an Agency?

With the basics of billing software out of the way, let's dig into why it can make such a big difference for an agency. With the increase in workflow and ever-evolving digitization, this type of software has become a survival kit for agencies and similar businesses.

  • Time-saving wizardry – Do you remember the days of manually creating invoices? With billing software, you don't have to. It automates the heavy work and leaves you with extra free time for more creative and interesting tasks.
  • Accuracy – With automation comes precision. These tools are meticulous, perhaps even more than people. They eliminate the chances of natural human error, like sending an invoice with the wrong amount or to the wrong client.
  • Cash flow clarity – Keeping track of who has paid and who hasn't can be tricky, especially as your list of clients grows. Billing software gives you a clear picture of your money inflow and clients. As a result, it's easier to plan and breathe easier about your cash flow.
  • Professionalism on display – Sending out sleek, professional-looking invoices reflects well on your agency. It shows you mean business, quite literally. Clients will trust you and will want to keep coming back.
  • Insightful reports – These tools can produce reports that give you valuable insights into the overall business health. It's a bit like a digital business consultant always on the call to supplement invoicing with data-driven advice.
  • Client-friendly features – Some billing software isn't limited to the accountant. Instead, it also lets clients view their own invoices, make payments, and even collaborate online. The software bridges the gap between you and the clients for friendlier billing.

How Do You Choose Billing Software for Your Agency?

Now you know what billing software does and what it does for you, the natural question to ask is, "How do you pick one?" To select the right software, you want it to fit your expectations and deliver quality results.

Here’s what you should look for:

  • Understand what you're after – First, map out what you need before committing. It depends on what your business does. Are you a small indie agency or a larger, more complex one? Should the software integrate with existing project management tools, or is it right to start from scratch?
  • Ease of use – The software should be intuitive and no more complex than a typical phone app. If it feels like you should've gone to school just to use the software, it's likely not the right fit. Look for a user-friendly interface that you and your team can figure out quickly.
  • Customization – No agency is exactly the same, neither in structure, culture, or the types of projects it undertakes. Therefore, the billing software may not be one-size-fits-all solution either. Look for software that lets you customize invoices and reports to fit the work your agency does.
  • Integration – The billing software should play nicely with other tools you use. While it doesn't have to integrate with everything at all times, integration with project management, CRM, and accounting software is a major plus.
  • Scalability – Think about the future. Your agency likely won't remain stuck at the same size and structure permanently. Therefore, you want software that grows with the agency. The software should be able to handle the extra load without a hiccup when the company grows.
  • Support system – While the billing software might work perfectly, most of the time, issues will arise. And when they do, you'll want access to top-notch customer support. Look for providers with solid support, whether through tutorials, a helpdesk, or a friendly chat service. Also, check their reviews and see what other customers have to say about their customer support.
  • Price point – Budget matters. A piece of billing software may have the best features, the most versatility, and astounding customer support, but it matters little if you can't afford it. Weigh the cost against what it offers and your long-term plans. But remember: spending a bit more can often save you a lot in the long run in terms of efficiency and capabilities.


Bonsai is an all-in-one software for billing invoices and so much more. Almost any agency can benefit from it, but it's particularly well-suited to freelancers and small agencies. But why is that, exactly? Take a look at its features and prices, and all will become clear.

What Are Bonsai's Key Features?

Bonsai lets you use countless pre-made invoice templates and also make your own. You can make free invoices, create automated reminders, and then get detailed reports on the billing and payments.

After you send invoices using Bonsai's templates, the software keeps on giving with time-tracking features. It lets you accurately track billing times down to a second. It's especially handy when you want to bill based on the actual time spent on a task.

While invoices and time-tracking are hugely convenient, security is above all else. Bonsai integrates simple and secure payments, including online payments through billing services like Stripe. Ultimately, it makes it easy to carry out transactions between agencies and clients.

Why Is Bonsai the Best Billing Software for Agencies?

Bonsai is one of the best billing software because it does so much with so little effort. It has a user-friendly interface and features that benefit most agencies, especially freelancers and small operations. In some ways, it replaces a personal financial assistant.

It also comes with a private client portal where you can securely share files with the clients and collaborate. This makes it an excellent pick for fostering client trust and continuous support.

The software can create and maintain thorough task lists collaboratively and track billing times accurately. Therefore, it's a robust and powerful tool for agencies that demand precision and efficiency, which is to say – all of them.

What Is Bonsai Pricing?

Bonsai is fairly flexible regarding payment options. There are three billing plans, each billable either per month or annually. The first is the starter plan that costs $21 per month when billed annually. It's perfect for freelancers who are just starting out. It includes basic features like invoicing, time tracking, client CRM, and expense tracking.

A step above basic is the professional plan, costing $32 per month if billed annually. Growing businesses will get the most out of this option. It includes everything already in the starter plan, plus extra features like workflow automation, a branded client portal, and integrating with QuickBooks, Calendly, and Zapier.

Finally, there's the business plan, which is for $66 per month if billed annually. This plan is great for small businesses and agencies that have already found their footing. It includes all the professional features, as well as subcontractor management, hiring agreement templates, and unlimited subcontractors.


QuickBooks is another billing software with quite a reputation. There are several features that make it appealing, but also a few drawbacks.

What Are QuickBooks' Key Features?

Firstly, QuickBooks lets you make custom invoices and manage payments. It's easy and efficient, requiring no more than a few clicks once you get started.

You can also easily track and categorize business expenses and automate other bookkeeping tasks. Track business mileage, inventory, and project profitability to report on expenses or identify and manage tax deductions. QuickBooks lets you do all that and more. Plus, it works with multiple currencies.

Why Are QuickBooks Limitations?

QuickBooks is feature-rich, but that can be a double-edged sword in some cases. The wealth of features might overwhelm some beginners or those whose expectations and needs are simpler. Furthermore, the service is cloud-based, so it needs a stable internet connection to keep everything in order.

What Is QuickBooks Pricing?

There are four primary pricing plans for QuickBooks: Simple Start, Essentials, Plus, and Advanced. Simple Start costs $15 per month (50% off for three months) and includes basic features like invoicing, expense tracking, and receipt capture. Essentials costs $30 per month (also with a 50% discount for the first three months) and adds billing management, time tracking, and multi-user support to the basic features. Plus, the plan costs $45 per month and includes everything in Essentials, plus inventory tracking and project profitability. Finally, advanced costs $100 per month but includes powerful reporting, custom access control, and automation for up to 25 users.


Stripe has changed the way agencies handle online transactions. Here’s a breakdown of some of its features.

What Are Stripe's Key Features?

Stripe's main feature is the embeddable checkout form that you can add to a website with just JavaScript. You can create and send invoices with built-in payment and charge your clients in over 135 currencies using various local payment methods. It's fast and secure, and lets you keep track of everything.

What Are Stripe's Limitations?

While Stripe has many advantages, it's not without its flaws. For one, it has policies in place regarding types of businesses, products, and industries that can or can't use it. This could be restrictive for some. Furthermore, its rate limits on the number of API requests may be somewhat limiting. For most APIs, Stripe allows for up to 100 reads per second and 100 writes per second. Finally, its structure might not be the most straightforward or cost-effective for B2B transactions.

What Is Stripe's Pricing?

Stripe's payment methods are fairly straightforward. There's the standard plan for 2.9% + 30¢ per successful charge for domestic cards. Then, there's the custom pricing plan for companies with large payments or unusual business models.


PayPal is a well-known name in invoicing and billing. Let's see why.

What Are PayPal’s Key Features?

PayPal offers cash back from many brands, which makes them attractive for buyers and, by extension, sellers. This program also includes a MasterCard virtual card without an annual fee. It's a safe and fast platform that operates in most of the world and can handle many currencies. It also includes payment options like "Buy Now, Pay Later."

What Are PayPal’s Limits?

PayPal charges fees for some transactions and these fees can sometimes be higher than with other similar services. The service can also impose limitations on the account depending on certain activities which aren't always transparent. Unfortunately, disputes are said to be time-consuming and not always fruitful. Another possible limitation is the existence of additional fees for some international transactions.

What Is PayPal’s Pricing?

PayPal doesn't have monthly fees and, therefore, no payment plans. Instead, it charges transaction fees, which depend on the type of transaction. It's convenient for agencies that like pay-per-transaction pricing.


Xero is another cloud-based accounting tool that is gaining traction with agencies. Let's see what it has to offer.

What Are Xero's Key Features?

Its best feature is the all-in-one paperless record keeping. It's safe and secure, centralizing finances on the cloud. It automates reconciling bank transactions and sending invoice reminders.

Not just for record-keeping, Xero can also give you trend analysis and customizable reporting. It can even pull bills and receipts automatically with Hubdoc.

What Are Xero's Limitations?

Some users who use Xero with large data files or high transaction volumes may encounter some slowdowns or lagginess at times. Furthermore, lower-tier plans may not cover everything a smaller agency or a freelancer is looking for. Lower plans also might not have bulk bank reconciliation.

What Is Xero's Pricing?

There are three main pricing plans for Xero. The Starter plan costs $29 per month for basic features. The standard plan costs $46 per month, while the Premium plan costs $62.


FreshBooks is a name you might've heard about already. They seem to be a common sponsor of business-themed content. But what makes them stand out? Let's take a look.

What Are FreshBooks' Key Features?

FreshBooks lets you customize invoices and send automated payment reminders easily. This is a standard feature, but it doesn't end there. It also gives you tools and reports to track the agency's profitability and cash flow health. It also lets you track expenses, time, and project collaboration. All of this is also available in a convenient mobile app.

What About Limitations?

FreshBooks is straightforward to get into, but it caters primarily to solo business owners, freelancers, and sole proprietors. It might not give as many benefits to larger companies and agencies. It might also have limitations for managing multiple departments or complex client structures.

What Is FreshBooks' Pricing?

FreshBooks has several pricing plans. The cheapest is the Lite plan, which costs $7.60 per month for the first six months and then $19 thereafter. It includes invoicing for five clients, tracking expenses, and payment processing. Plus, the plan costs $13.20 for the first six months and then $33, while Premium costs $24 at first and then $60. Finally, there's also a Select plan, which is priced at a custom price depending on the features you choose.

Square Invoices

Square is a convenient invoice and payment processing tool. Let's look at its features.

What Are Square Invoices' Key Features?

Like many other tools mentioned, Square Invoices creates and sends digital invoices and estimates, with an option for invoice scheduling. It accepts several payment methods, like credit and debit cards, Apple Pay, Google Pay, ACH bank transfer, and Cash App Pay. There's also a buy-now-pay-later option with Afterpay.

You can track the invoices in real-time, both paid and unpaid, and see estimates and contracts. It's all on a single dashboard.

What About Limits?

Square Invoices, like PayPal, charges different fees for different transactions, which might be a consideration for some transactions. Depending on the expectations, customization might be limited.

What Is Square Invoices' Pricing?

Square Invoices' basic plan is free. It has no monthly fees but allows for unlimited invoicing, estimates, and contracts. However, transaction fees apply. They're 3.3% + 30¢ for online card payments, 2.6% + 10¢ for in-person card payments, and 1% (minimum $1) for online ACH payments.

On the higher end, there’s a Plus plan that costs $20 per month for extra tools like multi-package estimates, custom invoice templates, and more. It's still subject to transaction fees. There's also a customizable Premium plan for a varying monthly fee.


Plutio is another comprehensive tool for business management. Here's what it does for agencies.

What Are Plutio's Key Features?

Plutio is an all-in-one suite to manage projects, collaborate in real-time, share files, create proposals, and get paid. It's also customizable, with branding, interface layout, and color choices.

The tool allows for real-time collaboration with communication tools, including comments, direct messaging, and project discussions. You can view everything in Kanban: cards, lists, tables, timelines, or a calendar. Plus, it supports over 25 languages.

Does It Have Limits?

While a neat tool, it might have occasional performance hiccups with large data and be somewhat limited in client management capabilities.

What Is Plutio's Pricing?

Plutio has three tiers of pricing. The Solo plan costs $19 per month and lets you invite up to three clients. The Studio plan costs $39 per month, with unlimited client invites and up to 10 contributors. The Agency plan costs $99 per month and lets you have 30 contributors.


Wave has convenient, free, easy-to-use accounting and invoicing features. Let's take a closer look.

What Are Wave's Key Features?

You can send invoices for free, including automated payment reminders. It also lets you track incomes and expenses, bank and credit card connections, and financial reports. You can also try some more advanced features, like receipt scanning, expense management, and payroll services with direct deposit and tax remittances.

Why Is Wave Great for Startups and Small Agencies?

While Wave is excellent for freelancers and agencies just starting out, some users might wish there were more options for customization that would aid in scalability. Also, there have been a few reports of limited customer support, which could affect some users.

What Is Wave's Pricing?

At Wave, invoicing and accounting are free. Per-use fees apply for payments, depending on the type of transaction. Mobile receipts cost $8 monthly or $72 as an annual fee. Bookkeeping support starts at $149 monthly.


Invoice2go is a mobile-first app for managing invoices. Let's look at what it brings to the table.

What Are Invoice2go's Key Features?

You can create and send professional invoices and estimates easily. Invoice2go supports credit cards, debit cards, and bank transfers. You can attach expenses, schedule appointments, and track billing hours. It's all available on the web, iOS, and Android.

Why Is Invoice2go Ideal for On-the-Go Agencies?

It's app-based, so it requires online connectivity, which might be limiting in some cases. Some companies might find it a little thin regarding customization.

What Is Invoice2go's Pricing?

The starter plan costs $71.88 per year ($59.99 per year with a 16% discount). It includes 30 invoices per year, card payment fees of 3.5%, free bank transfers (ACH), and client communication tools. Above it, the Professional plan is $119.88 per year ($99.99 per year with a 16% discount). It builds on the Starter plan with 100 invoices per year, lower card payment fees of 3%, and QuickBooks/Xero integration. Lastly, Premium plan costs $479.88 per year or $399.99 per year with a discount. It adds unlimited invoices, the lowest card payment fees at 2.9%, recurring invoices, and phone support.

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