.avif)
Ready to invest in AI?
Schedule time with Zeni's finance pros to learn more.
Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
Software specifically designed for SaaS accounting can help streamline your processes, monitor recurring revenue, reduce manual data entry, and avoid mistakes that could jeopardize the success of your business.
In this article, we'll explain why SaaS startups have different accounting software needs, and we'll also take a look at some of the best platforms for SaaS-based accounting.
What is accounting software for SaaS companies?
Accounting software helps businesses track their financial information through advanced technology and algorithms that take care of daily accounting tasks.
It allows users to manage income, operating expenses, and other financial transactions. Accounting software also provides features such as invoicing, payroll processing, budgeting, and tax preparation.
For SaaS startups, accounting software can provide the framework to manage customer subscriptions and handle billing and recurring payments.
Additionally, accounting software helps the company keep track of the usage of its services, understand customer trends, and develop reports for financial forecasts.
Why is accounting software important?
Accounting software is a vital tool for startups looking to track their financial information in an organized way. With software, founders can easily access the data they need when needed. Utilizing software also helps businesses save time and money by streamlining financial processes.
As a SaaS startup, you'll have access to insights and trends about your customer base and finances that can help you optimize your startup’s efficiency and make more informed decisions. Accounting software for SaaS companies ensures compliance with laws and regulations surrounding revenue recognition, taxes, and other financial matters. The IRS allows businesses to use accounting software records during examination too.
How is accounting software for SaaS companies different, and why?
While most good accounting software will help any type of business, with expense tracking and basic financial reporting, SaaS businesses need highly specialized accounting software due to a recurring revenue model and the complexity of subscription billing.
A SaaS accounting tool should include advanced features such as:
- Subscription/recurring billing or integrations with current subscription management software
- Customer payment integrations and reconciliation
- Customer lifetime value (LTV) analysis
- Daily bookkeeping capabilities to stay on top of the ever-changing customer lifecycle
- Advanced revenue recognition
These features help SaaS startups manage their finances more efficiently and competently by streamlining complex financial processes.
For example, imagine your customer signs a 12-month contract for a $100 per month plan and pays $1,200 upfront.
GAAP accounting—which involves accrual accounting, rather than cash basis accounting—requires you to recognize that as revenue only once you earn it.
For SaaS companies, that means you must initially record the payment you received as $1,200 of deferred revenue—a liability—then recognize $100 as revenue each month.
Halfway through the sixth month of the subscription, your customer upgrades to a $150 per month plan, paying $275 upfront to reflect their increased pricing for the rest of the contract. Without automation, your accounting team would need to do all of the following manually:
- Prorate the billing difference for the remainder of the sixth month (you’d collect an extra $25)
- Record a journal entry to add an extra $275 to deferred revenue
- Adjust the revenue recognition schedule so that it recognizes $150 per month for the remainder of the plan instead of $100
This can add up quickly when you have a high volume of customers. But with accounting software tailored for SaaS—such as Sage Intacct with a subscription billing module—these processes are automatic.
What are the benefits of accounting software for SaaS businesses?
While the best startup accounting software will allow any type of business to accurately track profits, cash flow, and generate basic financial reports, SaaS businesses need highly specialized accounting software due to a recurring revenue model and the complexity of subscription billing.
Due to a recurring revenue model and the complexity of subscription billing, B2C and B2B SaaS businesses can benefit from specialized accounting software to:
- Automate manual processes such as revenue recognition – SaaS customers pay subscriptions and add-on services fees, which require routine “maintenance” as customers upgrade, downgrade, or opt-in/out of different services.
- Provide SaaS-specific KPIs to investors – These include bookings, average contract value, customer lifetime value (CLTV), churn, ARR and MRR (annual and monthly recurring revenue), and more.
- Generate detailed GAAP-specific financial statement reports and forecasts.
- Provide real-time visibility into customer data and trends
Ultimately, the right accounting software can help SaaS businesses succeed. By streamlining tedious tasks and providing greater accuracy, startups can save time, reduce overhead costs, and make more informed business decisions.
Key elements to look for in SaaS-based accounting software
Finding the right SaaS-based accounting software can help you take complete control of your financial operation. When choosing cloud based accounting software for your SaaS startup, there are several key elements to consider. These include:
Automation
Automated features like invoicing, billing, payments, and reconciliation can help save you time and money and make your life easier.
These processes speed up transactions and ease financial management burdens so that you can focus on growing your business.
Recurring billing automation is especially important for a SaaS company. Instead of manually generating invoices monthly for all your customers, software can automatically issue them for you, apply usage-based charges, collect payments, and update your records.
For example, if a customer pays $50 per month plus a usage fee based on the number of active users, your system should be able to invoice them the proper amount each month, process the payment, and sync the details to your general ledger.
Take the time to determine if bookkeeping automation is available within the platform that best fits your needs to maximize efficiency in all aspects of your profit cycle.
Artificial intelligence (AI)
AI-based technologies can provide predictive insights into your finances. AI bookkeeping can help you identify opportunities and risks so that you can make better decisions in the future.
Good accounting software will offer features powered by machine learning to provide insights into operating expenses, burn rate, and other vital SaaS metrics.
Reporting
With good financial reporting capabilities, you'll be able to track important financial information and analyze customer trends in real-time. You'll also have insight into how well you're performing financially and other key metrics — all within a single platform.
Clear metrics and financial data will help you make efficient decisions regarding the direction and progress of your business.
.png)
Integration
Be sure your software works with your existing systems (like QuickBooks online or your corporate credit card) to create a connected, efficient system. When selecting a SaaS-based accounting solution, inquire about its ability to integrate with your other programs and tools.
Integration streamlines the data flow between software without extra manual input or effort. Automatic synchronization might also be possible, further increasing efficiencies.
Data security
Data security is another top feature to research thoroughly. You'll want to select a platform with robust security features and controls to prevent unauthorized access.
Look carefully into the encryption methods used by any SaaS-based accounting software, such as Secured Socket Layer (SSL). Remember to check the latest industry regulations to ensure adequate protection is available.
What are the best SaaS accounting software platforms?
When it comes to SaaS accounting software, a wide range of options are available. Some of the best accounting software for SaaS companies include:
- Sage
- Zoho Books
- Xero
- FreshBooks
- Zeni
*Ratings are based on Automation, AI, Reporting, Integration, and Data Security features.
Each platform has distinct features and capabilities, so take the time to investigate which solution is the best fit for your business. Consider critical features, cost, and scalability when making your decision.
Due diligence assures that you get the right SaaS-based accounting software to help manage your finances more effectively.
Here are some additional insights to help you find your ideal solution.
Zeni Pricing
Zeni’s bookkeeping subscriptions are all-inclusive, each providing AI bookkeeping, a dedicated finance team, onboarding and implementation support, plus a suite of financial products.
Pricing depends on your bookkeeping complexity, volume of monthly expense management, and annual revenue. You can get a 10% discount for paying annually, reducing your cost per year to between $5,928 and $8,628.
Sage Intacct Pricing
Sage doesn’t publicly disclose the pricing for its Sage Intacct plans, but based on third-party reports, their standard subscription costs around $9,000 per year.
However, you’ll typically spend around $15,000 to $35,000 for the features and user licenses you need. In addition, expect to pay $1.00 to $1.50 in implementation costs for every dollar of your subscription.
According to the 2025 SaaS CFO Tech Stack Survey, Sage Intacct is the second most popular core SaaS accounting solution after QuickBooks, used by 18% of all respondents.
However, it’s even more popular with larger companies, beating out all competitors among SaaS companies with an ARR of $11M to $50M.
Zoho Pricing
SaaS companies will most likely need the Ultimate Zoho subscription, which costs $240 per month and is the only Zoho plan that includes revenue recognition capabilities.
You may also need to pay another $59 for its Billpay functionality, in which case your annual costs would start at $3,588, plus implementation. Each additional user adds $2.50 per month.
Xero Pricing
Xero’s lowest subscription plan only allows you to send 20 invoices per month, so if you have more customers than that, you’ll typically need at least the $47 monthly subscription for unlimited invoices.
If you use multiple currencies, you’ll need the Established plan, which costs $80 per month. Depending on which plan you use, that puts your annual costs at just $564 to $960, plus implementation.
FreshBooks Pricing
If you want to send invoices to more than 50 clients per month, you’ll need at least the Premium FreshBooks plan, which costs $65 per month. That puts your annual costs at $780 plus implementation.
However, you can save 10% by paying annually, reducing your yearly subscription cost to just $520. In addition, each extra user costs another $11 per month.
How to Implement Accounting Software for SaaS
Here’s a step-by-step roadmap you can follow to help you implement your new accounting software for SaaS:
Phase 1: Planning and discovery (2–4 weeks)
- Define your business needs, compliance requirements, and reporting goals
- Choose an accounting platform and identify any necessary modules or add-ons
- Assemble an internal project team to manage the transition
Phase 2: System setup and configuration (4–8 weeks)
- Configure the new accounting system, including setting up subscription billing and revenue recognition schedules
- Set up integrations with the rest of your tech stack, such as payment processing and customer relationship management (CRM) tools
Phase 3: Data migration and testing (4–8 weeks)
- Migrate historical data, like transaction details, accounts receivable, payment history, and deferred revenue schedules
- Operate your systems in parallel for a month, comparing outputs to verify accuracy
Phase 4: Training and adoption (2–3 weeks)
- Conduct training for finance, operations, and leadership teams
- Finalize reconciliations between your new and old systems
- Transition to the new system for ongoing reporting
Migrating from a general accounting software to SaaS-specific systems may reveal issues like incomplete historical data or revenue recognition errors.
This is because many legacy systems can’t handle subscription billing or ASC 606 compliance. ASC 606 is the official Financial Accounting Standards Board (FASB) guidance on GAAP revenue recognition and the source of the infamous five-step framework for it:
- Identify the contract with the customer
- Identify the performance obligations in the contract
- Determine the transaction price
- Allocate the transaction price to the performance obligations
- Recognize revenue when (or as) the entity satisfies a performance obligation
Running your systems in parallel for a month or two is one of the best ways to identify and correct any discrepancies as you implement your new SaaS-specific solution.
It’s also beneficial to hire a strong team to oversee the transition, ideally supported by an expert in SaaS accounting standards. Depending on your internal expertise, consider hiring a fractional consultant’s accounting services.
Lastly, it’s a good idea to keep careful records of each step taken during the accounting process. In particular, document any assumptions you make due to any gaps in your knowledge.
Beyond accounting software alone: Working with SaaS finance experts
SaaS businesses have complex financial needs which require expertise to ensure accuracy and compliance.
Data must be tracked, reconciled, and reported to the correct stakeholders on time. This is difficult for most startups to accomplish on their own.
Accounting software can help streamline your financial processes through automation and AI insights. But even the best software cannot replace proper financial oversight.
For example, a finance expert can help you set up the most effective operating model to maximize your business’s growth.
A financial advisor can also familiarize themselves with your product, markets, and current environment to more accurately predict future performance.
While some startup founders may think they can get by without the help of an experienced finance professional, this is often not the case.
Working with a qualified SaaS finance expert can offer more efficient solutions to your accounting challenges and ensure accuracy throughout all your processes.
