15 Best Bookkeeping Software for Startups and SaaS Companies

This guide lists the top 15 best bookkeeping software for startups and SaaS companies. It explains how they suit different entrepreneurs based on their needs. The description explains the software product’s offerings along with a quick insight into who should use this and who should avoid it. The guide also lists a few add-on tools for startups and SaaS companies, along with a quick process to choose the best bookkeeping software and a few commonly asked questions about bookkeeping software for startups.

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15 Best Bookkeeping Software for Startups and SaaS Companies

Wrong bookkeeping setups lead to chaos, while the right one helps you scale finance without worrying about creating a bookkeeping system that handles everything important for your business.

This guide does two things intentionally. It explains the best bookkeeping software for startups and SaaS companies, and it also breaks down SaaS finance stack add-ons that solve problems core bookkeeping tools are not designed to handle.

Without delaying it any further, let’s dig in!

What best bookkeeping software for SaaS actually mean

Every bookkeeping software product is used to record transactions across all business cards and accounts, whether it’s debit or credit.

For startups and SaaS companies, bookkeeping software must do more than record transactions. It must provide you with a few more things, like a repeatable month-end close and subscription-based revenue inputs.

Startups require a clear audit trail for investors to bring in more funds. Startups require integrations with billing, payroll, and payables.

If a tool supports manual reconciliations, it’s as same as doing things on spreadsheets. Startups require bookkeeping products that support automations.

15 best bookkeeping software for startups and SaaS

1. QuickBooks Online – Best overall default for US startups

QuickBooks is the most common starting point for startups because it aligns with how finance talent is hired in the US. Most bookkeepers and CPAs know how to use QuickBooks; therefore, it reduces onboarding time and operational friction.

SaaS companies require an ecosystem that has everything in one place. Billing tools, payroll platforms, expense software, and revenue recognition systems integrate cleanly into QuickBooks.

Best for: pre-seed through growth-stage SaaS
Avoid if: If you already have these complicated needs, you’ll likely outgrow simple tools and need a more advanced finance setup

2. Xero – Best for collaboration and multi-user access

Xero works well for SaaS teams that want clean bookkeeping with broad internal and external access. Xero offers unlimited users. From the founder to operations manager to advisory, all get to see the financial picture of the business.

Its reconciliation workflows are strong, which matters when subscription payments flow in daily. Xero also integrates well with billing and payroll tools.  It’s just an alternative to QuickBooks with a lighter and easier operational feel with multi-user access.

Best for: teams with multiple stakeholders touching finance
Avoid if: if you’re already at the level where revenue recognition must be automatic

3. Zoho Books – Best automation value for lean SaaS teams

Zoho Books is a practical choice for startups that want structured automation without incurring high costs. It handles everything from invoicing, payments, to workflow automation.

It’s best when subscriptions are still simple, and you want to avoid a lot of manual finance work without needing a complicated setup.

Best for: cost-conscious startups with simple to moderate subscription models
Avoid if: if your subscription billing is already messy

4. Sage Intacct – Best accounting system for scaling SaaS finance

Sage Intacct is built for companies that have outgrown basic bookkeeping. It introduces stronger controls with cleaner money tracking options, without forcing you to switch to an expensive system.

It’s ideal for SaaS companies that have to ensure clean audits for investor reporting.

Best for: companies that have already raised serious funding
Avoid if: you care more about moving fast than setting up strict processes

5. Oracle NetSuite – Best for SaaS moving into ERP-level complexity

NetSuite is a big system used by SaaS teams across the globe to manage different groups of companies, teams, and products. It can track subscription revenue across different companies and product lines, and it creates very strict rules so reports stay clean.

This is not a simple starter tool. It is for companies that want a strong structure and are willing to set it up properly.

Best for: multi-entity SaaS and enterprise sales motions
Avoid if: you are early-stage or cost-sensitive

6. FreshBooks – Best for SaaS businesses with heavy services revenue

FreshBooks is a great bookkeeping software for recording your business transactions. If collecting money quickly from service clients matters, FreshBooks is an ideal choice for you while keeping things simple and smooth.

It is not built to handle complicated subscription revenue rules inside the accounting system. So it can be a good early option for a hybrid model, but not a strong long-term system for subscription accounting.

Best for: SaaS + services hybrids

Avoid if: subscription revenue recognition is your main challenge

7. Wave – Best free starting point for bootstrapped startups

Wave has anything that you need for basic bookkeeping for free. If you’re a startup founder working on a new idea or still operating in the pre-revenue phase, Wave can help you develop structures.

However, Wave is not designed to scale with SaaS complexity and should be treated as temporary.

Best for: pre-revenue founders
Avoid if: subscriptions, deferrals, or investor reporting are in play

8. Odoo Accounting – Best for startups embedding finance into operations

Odoo is best when you want your money tracking to connect closely with how your business runs day to day, like inventory, operations, orders, or internal workflows.

The catch is set up. If Odoo is set up poorly, your data can get messy, and that creates problems later. If set up well, it can feel like everything is connected.

Best for: product-led startups using Odoo across teams
Avoid if: you want a minimal setup system

9. ZipBooks – Best ultra-simple bookkeeping for very early SaaS

ZipBooks offers fast setup and basic reporting for founders who want structure without learning financial complexity. It helps early-stage teams stay organized before hiring a finance professional.

It is not designed for bigger companies, as it is more for owners who are trying to keep things neat until we get serious.

Best for: very early-stage SaaS
Avoid if: you need detailed reporting

10. Kashoo – Best for minimal bookkeeping needs

Kashoo is built for startups that don’t want to deal with a lot of financial configuration. It works when your business has low volume and your bookkeeping needs are basic.

It is a clean option if you want the minimum setup and you do not have complicated revenue rules. However, if your SaaS is growing fast or your subscriptions are getting complex, you will likely need something stronger.

Best for: solo founders or very small teams
Avoid if: subscription revenues are increasing

11. FreeAgent – Best for solo founders and micro-SaaS

If you’re an entrepreneur who’s looking for a bookkeeping software that has a clear dashboard with all the straightforward bookkeeping tools without paying a lot of money as an expense, FreeAgent is your best bet.

It helps you stay on top of basics and makes it easier to see what is happening with money. But it is not built for complicated subscription revenue recognition as you scale.

Best for: solo founders, micro-SaaS
Avoid if: you plan to scale rapidly

12. AccountEdge – Best for desktop bookkeeping preference

If you want a bookkeeping software that does not rely on the internet to access cloud-based servers for data and keeps everything on your computer, then AccountEdge is your best choice. Some teams like having local control and not relying on internet access for everything.

The downside is that it usually does not connect as smoothly with modern SaaS tools the way cloud systems do.

Best for: small teams preferring desktop accounting
Avoid if: you want modern SaaS integrations

13. Patriot Accounting – Best for payroll-centric small startups

If payroll is your biggest finance need, then Patriot is worth considering option for your startup. If your main regular money task is paying people and keeping simple books, it can be a practical choice.

It is not designed to handle complex subscription revenue rules or deep SaaS reporting needs, though.

Best for: payroll-heavy early-stage startups
Avoid if: SaaS revenue logic is complex

14. Bench (Software + Service) – Best for founders who want bookkeeping done for them

Bench is a bookkeeping software for entrepreneurs who don’t want to touch bookkeeping at all, but still need the right numbers for financial decisions. You get software plus real people who do the work.

The only downside is flexibility. If you need custom reporting or in-depth SaaS accounting, it can feel limiting as you’re not the one building systems.

Best for: founders who want hands-off bookkeeping
Avoid if: you need complex SaaS accounting

15. Microsoft Dynamics 365 Business Central – Best for SaaS teams on the Microsoft stack

Business Central is a full finance system that handles everything you need for basic bookkeeping, whether it’s general ledger and bank reconciliation. It’s the best option if you’re operating in the Microsoft ecosystem.

It also supports subscription and recurring billing workflows, which are useful when you bill customers on contracts or repeat cycles. 

Best for: SaaS companies that want stronger reporting and controls.

Avoid if: you need a super-fast setup, or you do not have time for implementation

SaaS finance stack add-ons

Once you’ve finalized a bookkeeping software for your startup, you need to stack a few add-ons to complete your system. Below is a detailed table of add-on tools that solve a specific SaaS finance problem that most businesses face.

How to Choose The Right Bookkeeping Software?

• Start by analyzing your current stage and operating reality.
• You need a tool that is easy to integrate with business operations.
• Your bookkeeping software should support a repeatable month-end close.
• Fast reconciliations and consistent reporting are a must.
• Pressure-test the system on deliverables.
• Pick the option that gives you accurate numbers on time, and a clear upgrade path as complexity grows.

Conclusion

QuickBooks is not the easiest tool, but it is often the practical choice to run a business when you can’t afford things to go wrong. Clean monthly closes, reliable reports, and a system your accountant can step into quickly. If you’re planning to switch to a different software, make sure you’re shifting because you need a change, not if you want a change for a different interface.