Best Accounting Software

As a leading CPA focused on startups, we’ve got some strong opinions on which accounting softwares are the best. In particular, for small, high-growth companies, QuickBooks Online is our typical recommendation.

Accounting Software Options

  • QuickBooks Online - this is the leading accounting software for smaller companies in the US for a reason. Highly-flexible, works great for remote companies (and virtual CPAs), connects with banks, credit cards, Paypal, payroll software. Really the best accounting software for startups and most small businesses.

  • QuickBooks Desktop - we no longer recommend this option. In particular, having a desktop software in the 2020’s is a bit of a backward statement about how seriously you take your books. That being said, the desktop version of QuickBooks is still pretty decent if you have a lot of inventory.

  • Xero - more popular outside of the USA than in it, Xero is the second best option for companies that want a cloud-based accounting software but who don’t want to pay a bundle. Xero also have solid connections via APIs into banks, credit cards, Paypal, payroll software. I used Xero for a while with some clients, and just found that QBO was a better option for US-based startups.

  • NetSuite - Netsuite is best for companies when they have any of the following criteria: you expect to have 100+ employees within the next 6 months; you have will $10M+ in revenue within the next 6 months; you’ve got over six domestic subsidiaries or international subs; you operate in high volume, high complexity industries such as FinTech, B2C SaaS, or eCommerce, manufacturing, hardware AND you meet 50% of one or more of the criteria above. We’ve got a handful of bigger, later-stage clients using Netsuite. It’s really an enterprise software, not for pre-Series C startups for the most part.

  • Sage Accounting - not the most modern UX, and the integrations may or may not work for your particular company. Some companies move up to the more expensive / robust / enterprise versions of Sage, but most of our clients choose NetSuite. 

  • FreshBooks - maybe an OK option for consultants and solo freelancers - but keep in mind, Kruze is a services/consulting firm, and we picked (and continue to use) QBO. 

  • Wave - an OK option for sole proprietors, but isn’t set up to sale.

  • Zoho Books - one of my VPs was talking with a small business owner (with a tech bent, but still, not VC backed, really a small business) where the founder was complaining about Zoho Books - He supposedly switched because it was cheaper than the QBO accounting software his bookkeeper recommended - and he ended up hating it, regretting his decision and worried about getting his books done on time to file taxes.

  • AI General Ledger Startups - There are maybe half a dozen startup AI accounting software vendors right now. We’ve demo’ed several of them, and have had startups come to us who wanted help getting off of the AI software and onto something more robust. Our current opinion is that these are not ready for prime time, and they are not as automated as you’d hope - these AI vendors seem to have focused on more advanced features, like revenue accrual, that most very early-stage companies won’t have to deal with. We’ll update this review if/when we find one that’s ready for a real startup.

Best Accounting Software for Specific Industries

At Kruze, we work with VC-backed businesses. These tend to cluster in specific industries - SaaS, crypto, eCommerce, biotech, hardware. Here are the best accounting software options by industry.

Best Option for SaaS companies

QuickBooks Online is the best accounting software option for SaaS companies. Software as a service businesses need to integrate specific billing and revenue systems - invoicing for B2B SaaS companies, and systems like Apple, Shopify, etc. for B2C ones. QBO is the best choice.

Best Option for eCommerce companies

QuickBooks Online is generally the best accounting software for small eCommerce businesses. As an eCommerce company gets bigger, it would make sense to upgrade to NetSuite, although Sage sometimes makes sense. However, these are overkill for a small business.

Best Accounting Software for Biotech Startups

Biotech companies can occasionally scale their accounting system needs more quickly than other types of startups. In general, a biotech company will most likely be best off starting with QuickBooks Online, but may transition to Netsuite or Intacct a bit more quickly than a SaaS or other startup.

What to Look For in An Accounting Software for Your Startup

When choosing an accounting software for a startup, there are several factors to consider:

  1. Scalability: Look for a software that can handle increased transaction volume as your startup grows; you don’t want to have to rip out a back office system in the middle of hyper growth. QuickBooks Online is a popular option that offers scalability.

  2. API connections: You don’t want to do manual data entry, and need an accounting software that connects directly into your banks, into your credit cards, into payroll - basically anywhere. Manual data entry causes errors, takes way too much time and dramatically increases the chances of fraud happening.

  3. Industry-standard system: Choose an accounting software that is widely used by accountants and professionals. You are likely going to switch from DIY books to using an outsourced bookkeeper to bringing this in house after the Series B or C. So you never want to be stuck with only a single or handful of accountants who can support your bookkeeping.

  4. Data portability: It’s important to own your company’s bookkeeping data and have the ability to access it even if you switch accountants or software providers. Own your data, make sure it’s easy to get to and download (and backup).

  5. Financial tracking and reporting: Look for features that allow you to track and report financial metrics. This is important for metrics-driven founders.

  6. Accrual or cash based accounting: VC-backed startups need to use accrual based accounting, but not every simple accounting software can really handle cash and accrual.

  7. Accounts payable and receivable management: Look for features that help you manage accounts payable and receivable efficiently. QBO has decent invoicing management, for example, although you will need to upgrade to a slightly more expensive version.

  8. User permissions and security: Go with a well-known vendor to ensure that the software has solid user permissions, security, privacy, and access controls to protect your financial data. You want it to be able to grant different levels of permissions, allow multiple users, etc.

  9. Customer support: Consider the level of customer support provided by the software provider. QuickBooks Online doesn’t have the best support, tbh, but the good news is that Kruze is a major user and distributor so we can usually get our questions answered. Usually.

Overall, QuickBooks Online is a recommended accounting software for startups due to its scalability, industry-standard usage, upgradeability, data portability, financial tracking and reporting capabilities, integration options, and user permissions and security features.

Accounting Software and Crypto

If you startup is transacting in DeFi, Web3, etc., you need additional accounting software to scalably run your bookkeeping. While QuickBooks and (most) of the other providers we mentioned automatically pull in bank, payroll and credit card transactions, the same can not be said for Crypto. These transactions need an additional “add on” software package to pull transactions into your general ledger. This may not be a big deal if you are doing only a couple of transactions per month (although there are possible tax implications to worry about), as you or your accountant can enter the data manually. However, we strongly recommend a specialized accounting software plugin if these types of assets are going to be part of your business. Read our Best Crypto Accounting Software piece to learn more.