Running a SaaS company comes with its own unique set of accounting challenges. You’re not just dealing with straightforward invoices or one-time payments; you’re managing recurring revenue models, subscription billing cycles, deferred revenue recognition, and often multi-currency transactions. If any of this sounds familiar, you’re already aware that traditional accounting software is insufficient for a SaaS business.

You require specialised SaaS accounting software that fits your company’s particular requirements if you want to succeed in a cutthroat and quickly expanding market. Why? Because accurate financial management isn’t just about crunching numbers; it’s the backbone of your growth, compliance, and scalability.

Here’s a quick reality check:

67% of SaaS companies struggle with revenue recognition compliance, and nearly 48% report errors in subscription billing cycles.

In addition to causing financial inefficiencies, these errors may also negatively affect customer satisfaction and possibly put you in hot water with authorities.

A system that automates time-consuming tasks and provides you with the real-time financial visibility you require to make better decisions is more important than simply managing your finances when selecting the best accounting software for SaaS.

This is where AI accounting tools are truly transforming the game. If you’re ready to level up your SaaS accounting, this guide will walk you through the 15 best accounting software tools tailored to meet your needs.

What to Look For in Accounting Software for SaaS Companies

Some accounting tools are better than others when it comes to handling the financial aspects of your SaaS company. Unlike traditional businesses, SaaS companies deal with recurring revenues, subscription models, and often operate across multiple countries. This means you need SaaS accounting tools that go beyond the basics and address these complexities head-on.

“The taxability of SaaS is not straightforward. In the United States, sales tax is generally applied to the sale of tangible personal property, but the classification of SaaS—being neither entirely tangible nor intangible—varies from state to state. Some jurisdictions treat SaaS as a taxable service, while others do not.”

Neil Bass, Managing Member at Bass Tax Group

When selecting the right accounting software for your business, you should prioritise the following:

1# Subscription Billing and Revenue Recognition

Your business is based on recurring payments, and keeping up with those subscriptions is necessary. Look for subscription billing software that can automate billing cycles and handle upgrades and downgrades seamlessly. Moreover, the software should be capable of tracking deferred revenue for accurate financial reporting. Revenue recognition software can help you stay compliant with ASC 606 and IFRS 15 standards, avoiding unpleasant surprises during audits.

2# Multi-Currency and Multi-Jurisdiction Support

Managing transactions in multiple currencies and navigating tax laws across jurisdictions can be very difficult if your SaaS company has international operations. Currency conversions will be automatically handled by the appropriate accounting software, which will also guarantee adherence to regional tax regulations. For international clients and subscription renewals, this is particularly important.

3# Automated Invoicing and Payment Reconciliation

No one has time to chase down unpaid invoices or manually reconcile payments. 

“Chasing unpaid invoices, especially by phone, feels “rude” to most of the people I meet in my classes. For some reason we feel uncomfortable when we have to ask for payment although really that is how the wheels of commerce work: providing a certain service or goods in return for a stipulated payment.”

Alberto Aleo, Sales & Marketing consultant

The best SaaS accounting tools will automate invoicing, send reminders to customers, and match payments to invoices without you lifting a finger. This improves cash flow management and reduces the risk of errors. Businesses that automate payment reconciliation see an average 40% reduction in manual accounting errors, according to a study by BlackLine.

4# Scalability for Fast-Growing Startups

Your SaaS business is growing fast. That means your accounting software needs to grow with you. So you need tools that can handle an increasing volume of transactions and users over time. You cannot sit back again to switch software when financial processes start getting more complex as your company scales. More precisely, a tool that works for 100 customers today should also work for 10,000 tomorrow.

5# Integration Capabilities with CRMs and Other SaaS Tools

Your accounting software shouldn’t work in isolation. It needs to integrate seamlessly with your CRM (like Salesforce or HubSpot) and other critical tools in your tech stack. Integration guarantees that you are not wasting time switching between systems. This will not only streamline your workflows but will also minimise data silos.

6# The Role of AI in Improving Efficiency and Compliance

This is where things get exciting. The artificial intelligence (AI) that powers contemporary SaaS accounting tools automates repetitive processes like revenue forecasting, fraud detection, and reconciliation. AI also guarantees compliance by seeing possible mistakes before they become an issue, which helps you avoid fines and penalties.

Tools like AccountsGPT use AI to manage everything from subscription billing to multi-currency transactions, giving you real-time insights while cutting down manual workloads by as much as 60%.

When choosing your accounting software, think of it as more than just a tool. It’s a partner in your SaaS journey. You’ll be able to scale your business more quickly and spend less time battling spreadsheets if you have the right features and AI-driven capabilities.

The 15 Best Accounting Software for SaaS Companies in 2024

With the increasing complexity of subscription-based business models, selecting the right accounting software for your SaaS company is more critical than ever. To make your decision easier, we’ve rounded up the top 15 tools tailored for SaaS businesses, evaluating them based on ease of use, scalability, AI capabilities, SaaS-specific features, and integration support.

1# QuickBooks Online

QuickBooks Online remains a favorite among startups and small SaaS companies. More than 29 million small business clients and over 80% of the accounting software market share are held by Intuit’s QuickBooks. It’s affordable and user-friendly. It offers solid basic accounting features like invoicing, expense tracking, and financial reporting.

• Best For: Startups and small SaaS businesses looking for simplicity.
• Key Features: Subscription management (limited), robust financial tracking, and numerous integrations.
• Drawback: Lacks advanced SaaS-specific tools like revenue recognition or AI-driven automation.

2# AccountsGPT 

AccountsGPT is revolutionizing SaaS accounting with AI-driven automation that not only streamlines workflows but also eliminates tedious manual tasks. By addressing key SaaS challenges like subscription billing, revenue recognition, and global compliance, it’s becoming a top choice for businesses at all growth stages.

• Best For: Small startups and enterprise-level SaaS companies that require scalable, AI-powered solutions.
• Key Features:
  • Automates subscription billing, revenue recognition, and GAAP compliance.
  • Offers real-time analytics for financial forecasting and managing deferred revenue.
  • Provides multi-currency support for SaaS businesses with international clients.
  • Seamlessly integrates with CRMs and SaaS tools.
  • AI-driven error detection

• Drawback: Still growing its user base, but adoption is rapidly increasing.

3# Xero

Xero was founded in 2006 and has grown to become one of the most trusted names in cloud-based accounting, serving over 3 million businesses worldwide (Xero Reports, 2023). Known for its intuitive interface and seamless integrations with tools. Xero offers a reliable accounting solution tailored to the unique needs of SaaS companies.

• Best For: Medium-sized SaaS companies that require basic financial management and integrations such as Stripe or HubSpot.
• Key Features: Expense tracking, invoicing, and reporting.
• Drawback: Doesn’t offer advanced AI features like AccountsGPT.

4# NetSuite by Oracle

Since its founding by Oracle, NetSuite has established itself as one of the most reliable ERP options for major SaaS businesses. With over 36,000 customers worldwide (Oracle, 2023), it’s praised for helping businesses streamline complex financial operations across multiple jurisdictions. Known for its scalability, NetSuite has received feedback for its ability to reduce manual processes by up to 40%.

• Best For: Large SaaS firms needing robust ERP and accounting software.
• Key Features: Advanced subscription management, revenue recognition, and multi-jurisdiction compliance.
• Drawback: Costly and has a steep learning curve for smaller companies.

5# FreshBooks

FreshBooks began with a mission to simplify invoicing and financial management for freelancers and small businesses. Unlike QuickBooks, which is solely designed for accountants, FreshBooks is for small business owners that’ll help them run their companies with this tool. FreshBooks is perfect for SaaS startups and freelancers who want an easy-to-use solution.

• Best For: Small SaaS businesses and solopreneurs.
• Key Features: Simplified invoicing and expense management.
• Drawback: Limited scalability and no advanced subscription management.

6# Sage Intacct

A trusted name in financial software, Sage Intacct delivers enterprise-grade reporting and compliance tools tailored for SaaS companies with complex structures. Scalability and comprehensive dashboards make it a favourite among expanding companies managing complex accounting requirements.

• Best For: SaaS firms managing large datasets or needing advanced reporting.
• Key Features: Customisable dashboards, revenue recognition, and ASC 606 compliance.
• Drawback: Steeper learning curve for beginners, extra cost for budgeting and reposting, limited customisation

7# Wave

Wave emerged as a top choice for early-stage SaaS startups by offering free yet powerful accounting features. It is a double-entry accounting tool. It’s ideal for startups that require affordable solutions without sacrificing financial clarity because it includes tools for basic reporting, invoicing, and scanning receipts.

• Best For: Entrepreneurs and startups looking for free accounting tools.
• Key Features: Free invoicing and bookkeeping features.
• Invoicing, Payment Integration, Automated Expense, Cash Flow Management, Mobile-Friendly Dashboard for Real-Time Tracking
• Drawback: Limited scalability for growing SaaS firms.

8# Chargebee

Chargebee is specialised in automating subscription management and recurring invoicing, and it was created specifically for subscription businesses. It is a preferred option for SaaS businesses with subscription-based business models because of its smooth integration with well-known tools like Salesforce.

• Best For: SaaS companies focused on subscription billing.
• Key Features: Subscription Management, Revenue Recognition, Tax Management, Payment Reconciliation, Customer Retention Tools
• Drawback: Region-Based Pricing, Conflict in Manual Pricing, Plan Deletion Restricted, Tax Integration Incompatible, Revenue Reconciliation Issues 

9# Zoho Books

Part of the Zoho suite, Zoho Books is a budget-friendly accounting software offering features like invoicing, tax compliance, and basic automation. Its ease of use and ability to integrate with Zoho CRM and other apps make it advantageous for smaller SaaS teams.

• Best For: Small businesses that already use Zoho’s suite of products.
• Key Features: CRM integrations and automated workflows.
• Drawback: Limited advanced features for scaling SaaS companies, no payroll services

10# Microsoft Dynamics 365

Dynamics 365 is a platform that integrates CRM and ERP features and is supported by the Microsoft ecosystem. For mid-to-large SaaS businesses that require integrated tools for customer management and financial operations, this makes it a strong option.

• Best For: SaaS companies needing a customisable and scalable system.
• Key Features: Subscription management and AI-powered analytics, advanced bank reconciliation, inventory optimisation
• Drawback: High cost and complexity for smaller firms, integration limitations, Requires a Microsoft ecosystem

11# ProfitWell

ProfitWell is specifically made for SaaS companies and concentrates on churn reduction and subscription metrics. It is perfect for both startups and large corporations, providing useful information about revenue and customer retention to maximise growth tactics.

• Best For: SaaS companies focused on churn reduction and pricing strategies.
• Key Features:Tools for subscription models, Data-driven insights, Revenue recognition, audit management, cashflow management
• Drawback: Doesn’t handle general accounting tasks, matrices difficult to understand, Limited Customization

12# Stripe Billing

This tool is created by the same people who created Stripe. Stripe Billing is a robust payment management solution designed specifically for SaaS businesses that operate on subscription models. This tool streamlines billing complexity by automating subscription management, recurring payments, and invoicing. A unified ecosystem for revenue and payment management is provided by its smooth integration with other Stripe products.

• Best For: SaaS startups prioritising seamless payment solutions.
• Key Features: Subscription Management, Detailed Analytics, Multi-Currency Support, Developer-Friendly APISeamless Integration
• Drawback: Limited accounting features.

13# Bench

Bench is an accounting and bookkeeping service created to make small business financial management less complicated. Bench’s user-friendly platform and committed team of bookkeepers take care of routine bookkeeping duties, freeing up startups to concentrate on expanding their companies.

• Best For: Startups that prefer a hands-off approach to bookkeeping and accounting.
• Key Features: Dedicated Bookkeepers, Tax Season Support, Intuitive Dashboard, Customized Reports
• Drawback: Lacks SaaS-specific features like revenue recognition.

14# Intuit TurboTax Business

The tax-focused software TurboTax Business was developed by Intuit with the goal of making tax filing easier for small businesses. In order to maximise credits and deductions and guarantee accurate filings, it provides expert assistance and guided steps.

• Best For: Small SaaS companies that need assistance with tax filing.
• Key Features: Step-by-Step Guidance, Smart Deduction Finder, Built-In Support, E-Filing, Integration with QuickBooks
• Drawback: Focuses on tax filing and lacks broader accounting tools for managing financials beyond tax season.

15# Kashoo

Kashoo is a basic accounting tool made for startups looking for affordability and ease of use. Kashoo’s user-friendly design makes it easy for businesses to handle basic accounting, expenses, and invoicing without being overly complicated.

• Best For: Businesses looking for an affordable, no-frills solution.
• Key Features: User-Friendly Interface, Expense Tracking, Invoicing, Cloud-Based Access, Affordable Pricing
• Drawback: Revenue recognition tools, multi-entity support, and other SaaS business-scaling features are missing.

Comparing SaaS Accounting Tools: Which is Right for You?

Choosing the right SaaS accounting tool is determined by your company’s specific needs, such as size, growth stage, and requirements. To assist you in making an informed decision, here is a feature comparison table that summarises key aspects of all 15 tools.

Making the Right Choice

• For Small Startups: Wave, FreshBooks, and Kashoo are affordable solutions that efficiently manage simple accounting requirements. For bookkeeping, Bench is a good option if you like a more detached approach.
• For Growing Businesses: SaaS companies that are rapidly scaling will benefit from Xero, Chargebee, or Zoho Books. These tools offer a good balance of affordability and robust features like multi-currency support and automated workflows.
• For Enterprises: Larger companies with complex requirements should look into NetSuite or Sage Intacct for advanced reporting, compliance, and multi-entity support.
• For AI Enthusiasts: AccountsGPT stands out with its AI-driven features, making it ideal for tech-forward startups aiming to automate accounting and gain actionable insights.
• For Subscription-Based Models: Stripe Billing and Chargebee are tailored for SaaS companies focused on subscription management and recurring payments.

No worries if you’re still unsure. Simply list out the challenges and tasks you need help with, and get in touch with Gaper. We’ll help you create a custom LLM tailored to your unique needs and budget.

Conclusion

Having the best accounting tools for SaaS is now essential in the rapidly evolving SaaS market. With subscription models, multi-currency transactions, and complex revenue recognition processes becoming standard, traditional accounting methods can no longer keep up. A survey conducted by Intuit’s QuickBooks revealed that 98% of accountants and bookkeepers used AI in the past year. 

There are firms out there that have invested nearly $25,000 on average in accounting technologies. As the industry continues to grow and evolve, staying ahead of the curve with advanced accounting tools will be crucial for success.

AI-driven solutions enable you to concentrate on expansion without being distracted by accounting hassles, regardless of your organisation’s size. The key to choosing the best SaaS accounting software in 2025 lies in understanding your unique needs. Regardless of where you stand, investing in the right tool today can save you time, money, and stress tomorrow.

FAQs: Everything You Need to Know About SaaS Accounting

What is the best accounting software for SaaS startups

Your business’s size, complexity, and objectives will determine which accounting software is best for SaaS startups. Small startups can find affordable, user-friendly solutions with Wave or Kashoo. More sophisticated solutions that manage billing automation and multi-currency transactions, such as Xero and Chargebee, may be advantageous for expanding SaaS businesses. For tech-savvy startups looking to stay ahead of the curve, AccountsGPT stands out as a powerful AI-driven tool that provides automation, advanced analytics, and scalability tailored for SaaS businesses.

How does AI improve SaaS accounting?

SaaS accounting is revolutionised by AI, which saves time and money by automating time-consuming processes like data entry, invoicing, and reconciliation. Tools like AccountsGPT leverage AI to provide real-time financial insights, streamline SaaS-specific processes like revenue recognition, and enhance accuracy in tax compliance. AI also adapts to your business’s unique patterns, making it easier to forecast cash flow, identify trends, and make data-driven decisions.

Can I use AccountsGPT for subscription billing and multi-currency transactions?

Absolutely. AccountsGPT is designed with SaaS businesses in mind. It supports multi-currency transactions and subscription billing with ease. In addition to automating repetitive invoicing procedures and guaranteeing accuracy when processing international payments. It interfaces seamlessly with your current payment systems.