The 3 Best Accounting Software Options for SaaS Businesses

3 Best SaaS Accounting Options

The best SaaS accounting software combines scalability with automation tools and a platform that can support a variety of different business types. Our top picks are:

  1. QuickBooks Online
  2. FreshBooks
  3. Xero

How many of us really like dealing with the nitty-gritty of running the accounting and bookkeeping operations of our companies? Unless you’ve got a passion for numbers (or you’re the founder of an accounting startup), you probably look at accounting as the least engaging, most time-consuming part of your day-to-day as an entrepreneur.

But just because you might battle with your business accounting software doesn’t mean you get a pass on using it. This is particularly true if you’re in the Software as a Service (SaaS) space, where keeping track of your money is no easy feat. You’ve got client invoices to manage, vendors to pay, and—if you’re really crushing it—plenty of growth in your future.

So how do you keep track of your daily business accounting while also gearing up your business for future growth? You pick the best accounting software for SaaS companies.

We’ll show you our top choice for the best accounting software for SaaS companies, why we chose them, and a few alternatives to consider.

What to Look for in SaaS Accounting Software

It’s not easy to wade through all of the SaaS accounting software options. There’s a bevy of platforms to choose from across every operational aspect of your company. Onboarding each of them requires a ton of setup, and spending the time to learn their nuances. Then, of course, there’s the cost of purchasing licenses to consider.

And finding the best accounting software for SaaS companies is doubly hard: You have even more options than other types of small business owners do, and figuring out the differences among all these accounting software packages is tricky at best.

However, there are a couple of key things that differentiate the best SaaS accounting software options from the rest of the crowd. They are:

  • Scalability: Most SaaS companies are growth-minded, meaning you need an accounting software that can keep up with your business as it expands.
  • Automation: SaaS is a fast-paced industry. Nobody wants to spend all their time doing accounting, so you need a solution that is as high-tech as the service you provide. Automation allows you to focus less on your books and more on your business.
  • Multi-Business Support: SaaS encompasses a wide range of business types. Your software needs to provide a solution that can account for that.

Best Accounting Software for SaaS Companies: Top Picks

Now that we know what to look for, here is our top pick for the best accounting software for SaaS companies:

QuickBooks Online

One of the top options for the best accounting software for SaaS companies is QuickBooks Online.

You’ll have a hard time finding a platform that’s as scalable as QuickBooks Online: The software offers different levels of support that accommodate your company’s evolving needs as it expands. Plus, the setup is easy and the bookkeeping is intuitive.

Getting more specific, there are several reasons we think QuickBooks Online is such a good option for SaaS companies. We’ll list them here:

1. QuickBooks Online Requires No Manual Data Entry

We had a chance to chat with Scott Snyder, founder and CEO of Sellution, about how he chose the accounting software for his SaaS company. Snyder says the biggest deciding factor was manual data entry.

“Ultimately, I want to build a data highway between my company and the accounting platform,” Snyder says. “When I start thinking about what that looks like, I immediately get concerned about whether or not I’m going to outgrow the solution.”

Snyder says that another deciding factor in finding Sellution’s SaaS accounting software was how well the software could integrate with other platforms. “I also had to identify limitations of the program’s API framework, and whether or not we can build a seamless integration between them,” he says.

Luckily, QuickBooks Online offers an open API, which means you can connect your software directly with the platform to push and pull data with zero effort.

2. QuickBooks Online Grows With Your Business

Finding an accounting software platform that will scale as your company grows is another major consideration you need to make as a SaaS company (and, quite frankly, as a business owner in any industry).

If your accounting program can’t grow as your company expands, sooner or later you’ll be forced to migrate to another platform. This is a huge undertaking, but you can avoid that headache by finding the right accounting platform from the get-go.

QuickBooks Online offers a seamless experience to support your needs as your business expands. When you’re just starting out, you can use the basic level, Simple Start, to record your start-up expenses. As you get ready to launch, you can upgrade to Essentials or Plus, depending on your needs.

3. QuickBooks Online Makes It Easy to Track Your Financial Health

Another major consideration when picking the best accounting software for your SaaS company is generating custom financial reports easily.

“When I logged into QuickBooks Online,” Snyder says, “the first thing I saw were colorful gauges and statistics on the platform’s dashboard. I wondered if I could drill into the numbers, and QuickBooks Online had me covered. With a simple click, I was viewing a fully customizable report that I was able to export or send via email.”

Like Snyder, you’ll want to (if not need to) keep tabs on your weekly, monthly, and quarterly financial health, and that means digging deep into your books to make sure everything’s running smoothly. QuickBooks Online shines in this regard, as it supports fully customizable reports. Their intuitive interface shows you the information you need to know with minimal fuss.

4. QuickBooks Online Has a Helpful Virtual Community

Although the software itself is top of the line, what we really love about QuickBooks Online as a SaaS accounting software is the robust community of QuickBooks Online users.

Most of those users are active on online forums, and they’re more than willing to help answer questions about reporting, integrations, and general help with navigating the platform.

In fact, there’s a QuickBooks Online forum for just about any question—all you need to do is know where to ask. There’s even a ProAdvisor community for particularly tricky questions. Plus, QuickBooks ProAdvisors are bookkeepers, consultants, CPAs, and other tax preparers with certification on the platform, meaning they can go the extra mile to help you get set up and run your business’ bookkeeping.

So, if you run into sticky spots with your SaaS accounting software, know that help is just a click away.

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Best Accounting Software for SaaS Companies: Alternatives

Although we feel SaaS companies can do very well with QuickBooks, if you’d prefer to explore your options, there are two additional products we recommend.


FreshBooks is designed specifically for small businesses, so if your SaaS company is still in its early stages, this could be a good option. FreshBooks offers three different small business accounting solutions—Lite, Plus, and Premium. Each option is designed for businesses in different stages of growth, with the Lite plan being the least expensive and the Premium plan being the most expensive.

The features you get with FreshBooks depend on the plan you sign up for, but all plans come with the following features, which are essential for SaaS accounting:

  • Invoicing (including recurring invoices and late payment reminders)
  • Automated expense tracking
  • Time tracking
  • Collaborative tools (file sharing, centralized product conversations)
  • Payment processing
  • Reporting (P&L statements, accounts aging)

FreshBooks is available at a price that is comparable to QuickBooks, and it features very similar accounting functionality. This makes it a great alternative to consider for those looking for SaaS accounting. For a limited time, FreshBooks is offering 70% off for the first 3 months when new users skip the 30-day free trial period.

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Xero is another popular option. Like FreshBooks, there are three different Xero plans you can choose from—Xero Early, Xero Growing, and Xero Established—each suited for businesses of different sizes. Features you can expect with all plans include:

  • Invite collaborators to work on your Xero account
  • Create a variety of business financial statements
  • Mobile app
  • Sync all business bank accounts
  • Extend the functionality of your service via the Xero app store
  • 24/7 customer support

Xero also offers a 30-day free trial. We recommend giving it a test run. If it’s not to your liking, switch over to QuickBooks or FreshBooks for your SaaS accounting needs.

Picking the Best SaaS Accounting Platform for Your Business

Whether you’re just forming your SaaS company, or have begun to hit your stride and need a seamless way to manage your finances, QuickBooks Online provides a robust way to manage your company’s money from top to bottom.

In particular, we recommend QuickBooks Online as the best accounting software for SaaS companies because:

  1. Its cloud-based API lets you effortlessly enter and update your data.
  2. The platform seamlessly scales along with your business.
  3. Its intuitive interface makes it easy to see, analyze, and generate reports on your company’s financial health.
  4. An active community of QuickBooks Online users is available to answer your questions 24/7.

If you find QuickBooks is not to your liking, you have two solid options in FreshBooks and Xero. No matter which software you choose for your SaaS accounting needs, before you set out on your search make sure you know precisely what you need your accounting software to do for your business. Keep your personal tastes in mind, as well. G2 Crowd, a business software review site, has thousands of reviews of top accounting software, including QuickBooks Online, FreshBooks, and Xero. It should be a first stop as you compare options. Better to do your homework now than undergo a painful migration later!

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Contributing Writer at Fundera

Stacy Kildal

Stacy Kildal is a contributing writer for Fundera.

Stacy Kildal is owner/operator of Kildal Services LLC—an accounting and technology consulting company that specializes in all things QuickBooks. From 2012 to 2017, Stacy has been named one of CPA Practice Advisor’s Most Powerful Women In Accounting. 

Stacy is one of the three hosts for the QB Show and has also been featured frequently on Intuit’s Accountant Blog, Community “Ask the Expert” forums, at various Intuit Academy To Go podcasts, as well as hosting a number of Intuit Small Business Online Town Hall sessions. 

She is a big fan of working mobile and has been recognized by Intuit as being an expert on QuickBooks Online, having written Intuit’s original courses for the U.S., Singapore and Canadian versions.

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