The Best Startup Accounting Software for SaaS Startups

Josh Leider

Josh Leider, Head of Growth at Graphite

As a SaaS organization, you’re leading the charge in technological innovation. A dedication to being at the forefront of technology is likely an integral part of the DNA of your startup. But this dedication to technology should extend past the scope of your product and into all areas of your business. 

Technology is critical across your startup’s finance and accounting initiatives.

So what is the best startup accounting software to help you keep your books in order, help you achieve tax compliance, and boost your efficiency?

Before we get into our recommendations, let’s talk about some key considerations when selecting accounting software for your SaaS startup.

How to Select Startup Accounting Software

With the explosion of options for technology out there now, it’s more important than ever to be intentional about selecting the right accounting software. 

In addition to making sure that your tools have the basic functionality and features that you need, there are a few other considerations that are especially relevant to you as a SaaS organization. 


Whether you’re currently experiencing growth or are ramping up to raise funds so that you can get to that next level, you need to make sure any technology you get grows with you

Failure to acknowledge the possibility that your current needs may look very different in a year or even a few months can lead to wasted resources—both financially and with the time you invest into implementing it. 

To avoid any headaches, make sure you select an accounting software that is adaptive and can suit even the most complex financial situations. Startup accounting software doesn’t always mean small scale—it means that it can flex to fit startups in the many stages they go through. 


You’re a SaaS organization, so integrations are important as you know. Your startup likely has many existing systems that you use to stay on top of your finances (a PEO, an invoicing platform, etc). When you’re considering a new tool to add to the stack, you want to prioritize trusted integrations. 

When everything integrates seamlessly—from your accounting software to payroll to accounts receivable—you spend less time manually jumping back and forth between tools and more time on the financial processes that matter.   

Data Analytics and Reporting

A strong accounting strategy extends far beyond simply keeping a record of the money coming in and out of your company. The startups that are best positioned for growth use their financial data as fuel for decision-making. 

To leverage your financial data, you want to make sure that your accounting software offers robust reporting and analytics. While you may bring on a dedicated tool for these strategic processes, native reporting in your financial tech is helpful for in-the-moment analysis. 


Technology is evolving at a fast pace. Just look at the speed at which artificial intelligence has been adopted across industries in the past year. Many SaaS startups have been agile in their efforts to integrate AI into their products, and that forward-looking focus is what makes those solutions attractive to work with. 

You don’t want to select a software solution that has been stagnant for years. Seek out a product that is constantly being innovated and improved. If you are strategic about selecting a piece of technology that evolves as the times do, you will reap the benefits. 

Why Does Accounting Software Matter for Startups?

Accounting is the backbone of your organization’s finances. No matter how tight your processes are in other areas of the business, if your accounting processes are not in order, it sabotages your ability to make critical operating decisions—or even to stay in business. 

That’s why there’s a lot of pressure to get accounting software right. 

Accounting software stores, organizes, and manages all of your startup’s financial operations. You’ll use this software to record transactions and produce basic financial reports like P&Ls and balance sheets. You’ll eventually use the information housed in this system to file your taxes. 

Accounting software, specifically curated to your needs as a SaaS startup, will create reliable processes that ensure your team is:

  • Compliant with tax regulations
  • Not burning cash too fast
  • Able to access all of the data you need to plan for the future

You have to find accounting software that seamlessly integrates with your existing systems while meeting your most pressing needs. When you find the right fit, this software will help your startup maintain financial health and stability. This will show well for investors, but it will also allow you to focus even more on growth and innovation for your organization.

Technology is just one piece of the puzzle. Strategy is what matters most.

What Is the Best Accounting Software for a SaaS Company?

There is no shortage of accounting software out there for you to pick from. With all of these options, it can be a little intimidating to know which is the right one for you. 

As financial experts who work closely with startup clients who are in these tools noticing their strengths and weaknesses every day, the top contenders have become very clear. 

Quickbooks Online

Quickbooks wins the #1 spot on this list for early-stage and high-growth startups alike. 

We find that this software has the most comprehensive range of features that are custom-tailored to the unique needs of rapidly evolving SaaS businesses. 

It is scalable, cloud-based, and easily integrates with a range of the most-used business tools in SaaS companies. Additionally, it’s extremely user-friendly, which makes it easy for anyone on your team to jump in and find the features they need. 


Rillet is another incredible startup accounting software because it was designed precisely for SaaS startups. 

The platform is feature-heavy, giving teams the ability to sync with a variety of systems, analyze their data, and stay on top of all of their financial operations. They also take advantage of the latest tech innovations—namely, AI—which is attractive to SaaS startups who want the best-in-class solutions. 

The interface is also extremely clean and easy to navigate, despite its advanced capabilities. 


For the SaaS startups with slightly more complex operations, we’d highly recommend NetSuite

This tool has the widest range of features that cover not just accounting, but also ERP, CRM, and e-commerce capabilities. This range makes Netsuite an attractive choice for a unified platform for managing various business processes.

Netsuite is also customizable and flexible. While teams with simpler operations may prefer more of a plug-and-play approach, teams with more complex operations need a solution that is custom-fit to their needs. This tool fulfills this need while eliminating the necessity of hiring someone to build a custom solution from scratch. 

Startup Accounting Software Is Just the Beginning

The accounting software you select, while critical, is just the beginning of your startup’s growth journey. You also need reliable and strategic financial and accounting processes. 

The best way to reach even the most aggressive business growth goals—whether you’re early-stage or several years into your journey—is to bring on a financial pro to point you in the right direction. 

Graphite provides accounting services, fractional CFO support, and tax compliance guidance to help startups forge a strong foundation. 

Need CFO or Accounting Help?

Born out of a VC fund, Graphite fully understands the strategic and financial needs of high growth companies. If you need accounting support or simply have a question about accounting at your company, feel free to connect with us!

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