5 Top Picks for Ecommerce Accounting Software


Paul Woodland


Reviewed by


March 24, 2022

This article is Tax Professional approved


When you start an ecommerce business, nothing feels better than that first sale.

And then the next.

And then realizing your side hustle might actually be a legit business.

But then you realize you need to do legit business things—like accounting. Though staying on top of your financial data may not be very exciting, it's the best way to keep the IRS off your back and avoid an audit.

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If this sounds familiar, we’ve got you covered. Here are the five best options for accounting software for ecommerce businesses, so you can stop stressing about the books and start trying to catch up to those runaway sales.

How ecommerce accounting software can help you scale your online business

Accounting software is a tool you can use to track all your transactions and generate financial reports. Of course, you might already know how important this is to any business, but ecommerce presents some specific accounting challenges.

Depending on your online business, you could have tons of transactions to keep track of. If you were using a paper bookkeeping system and trying to do it all yourself, this could easily prove overwhelming.

Accounting software alleviates this administrative burden by integrating with your seller platform and automatically importing transaction data into its system. These imports can make bookkeeping much faster while reducing the risk of any data-entry mistakes you might make while transferring over your data. That accurate data comes in handy in the unlikely event that you face an IRS audit.

Small businesses also need to consider whether they are doing business in other states or countries when choosing their accounting software. Different jurisdictions have different tax laws and rates, and you might be required to keep track of sales tax outside of your business’s home state. The best accounting software for ecommerce will automatically keep track of sales tax for each state, so you don’t have to worry about it.

If you want to save countless hours of data entry and be prepared at tax time, reliable accounting software is essential for your ecommerce business.

Our top picks for the best accounting software for ecommerce

While these aren’t the only accounting software options available, they’re some of the best based on specific features your ecommerce business might require.

All of these picks offer small business accounting tools like basic financial reporting and automation when it comes to importing bank transactions.

  1. Most comprehensive solution: QuickBooks Online
  2. Best free accounting software: Wave
  3. Best choice for service-based businesses: FreshBooks
  4. Best for multiple users: Xero
  5. Best hands-off solution: Bench

Most comprehensive solution

QuickBooks Online

First up, we have QuickBooks Online, a completely cloud-based bookkeeping and accounting solution that offers multiple levels of pricing and features.


QuickBooks integrates with bank accounts, payment processors and aggregators (like PayPal), and major ecommerce platforms like Shopify and WooCommerce. This automation saves you a ton of time by not requiring you to transfer or enter data manually.

Tracking the different sales tax rates and balances can quickly become overwhelming if you’re selling in several states. Luckily, QuickBooks automatically calculates sales tax across multiple jurisdictions regardless of your business’s home state.

A product-focused ecommerce business could find QuickBooks appealing for a few unique features: purchase order functionality and inventory tracking. If you work with larger suppliers, you can issue purchase orders when buying on credit—most of our other options aren’t capable of handling purchase orders.


QuickBooks is so feature-rich that it can be overwhelming—it’s easy to make an accounting error if you’re not as experienced with bookkeeping. Online reviews indicate that customer support is limited, so while their support database is quite large, it can be frustrating trying to navigate and fix your error on your own.


QuickBooks Online splits its features up into four tiers of pricing:

  • Simple Start: $25/month
  • Essentials: $50/month
  • Plus: $80/month
  • Advanced: $180/month

Who QuickBooks Online is best for

QuickBooks is best for those who see their business growing into a larger enterprise and don’t mind investing some time into learning the system or already have some experience with bookkeeping. It could also be the right accounting software for anyone running a product-focused online store.

Best free accounting software

Wave Accounting

Next, we have Wave, a basic (but completely free!) accounting software option with limited features.


Wave offers basic accounting features like invoicing and expense tracking. It even integrates with your bank and credit cards to accept and deposit payments and automates bank reconciliation. Although standard payment processing fees apply, the bookkeeping features are entirely free.

Wave may be a simpler set of accounting tools, but set up is relatively quick. Its free option comes with standard dashboard and financial reporting capabilities that allow for real-time financial insights using Wave’s handy mobile app.


Wave’s biggest downfall for ecommerce businesses is that it doesn’t natively integrate with seller platforms or offer more advanced features—in a sense, you’re getting what you pay for. You can always add more functionality with Zapier integrations, but that setup is a lot more time-consuming than many other accounting programs.


Did we mention it’s free? Wave’s base plan costs nothing, but if you want to add payment processing or payroll, you can upgrade as follows:

  • Free: $0/month
  • Payment Processing: Pay-Per-Use
  • 2.9% of transaction + 30c per transaction for Visa + Mastercard
  • 3.4% of transaction + 30c per transaction for American Express
  • 1% of transaction ($1 minimum) for bank account payments
  • Payroll: Monthly
  • $20/month + $6 per employee or independent contractor if in a self-service tax filing state
  • $35/month + $6 per employee or independent contractor if in an automatic tax filing state

Who Wave is best for

Although a barebones option, Wave is a good choice for small businesses on a tight budget that are okay with the lack of integration.

Related: Best Free Accounting Software for Small Businesses

Best choice for service-based businesses


FreshBooks started primarily as invoicing software but has since come a long way. Although it now offers most accounting features, FreshBooks still aligns better with service-based ecommerce businesses like custom crafts, online coaching, or other individualized online businesses.


Like QuickBooks, FreshBooks can link to your bank account and payment systems to automatically import transaction data to save time and add accuracy. It even offers major financial reports like balance sheets, profit and loss statements, and cash flow statements.

However, FreshBooks’s greatest strength lies in its project management features. FreshBooks allows you to set up projects, track the time you or your team spend on them, and then seamlessly export that data into invoices upon project completion. This functionality could be ideal if your ecommerce business sells made-to-order goods or hourly services.

FreshBooks also includes customizable invoice templates to save small business owners from fiddling with time-consuming spreadsheets.


FreshBooks’ service-focused feature set means it’s not necessarily the best fit for product-based businesses. It doesn’t offer inventory management or automatic adjustments to sales tax based on buyer location.

It also doesn’t integrate natively with ecommerce platforms, making it a poor option if you primarily sell physical goods.


FreshBooks offers a multi-level pricing structure. Lower tiers limit the number of billable clients, while higher levels include more advanced features.

  • Lite: $15/month, 5 billable clients
  • Plus: $25/month, 50 billable clients
  • Premium: $50/month, unlimited billable clients
  • Select: Custom pricing for enterprise clients

Who FreshBooks is best for

With its available features and pricing structures, FreshBooks is a great choice for self-employed freelancers, like Etsy or eBay sellers, who operate a project-based ecommerce business. Those project management features, including time tracking and invoicing, also make FreshBooks a good fit for service-focused businesses.

Best for multiple users


Xero is another cloud-based accounting suite that gives QuickBooks a run for its money. It offers a complete feature set like QuickBooks, but at a fraction of the cost.


At first glance, it might seem like Xero is just a cheaper version of QuickBooks, but Xero’s unlimited user seats offer a serious advantage. This is helpful if you have a team to help you manage your ecommerce business.

Xero is an appealing choice for both product-based and service-focused ecommerce businesses since it includes inventory management and project management tools. You might consider it a blend between QuickBooks for products and FreshBooks for services.


Unfortunately, Xero can’t automatically calculate and track sales tax based on buyer location, nor can it integrate natively with Shopify. If you’re selling many products in several different states, you might want to opt for another option.


As mentioned earlier, Xero does beat QuickBooks when it comes to pricing, offering three levels to choose from:

  • Early: $12/month
  • Growing: $34/month
  • Established: $65/month

Who Xero is best for

Xero is best for businesses with a large team or those that want most of the features of QuickBooks without its price. It could also be a good fit if you sell a mix of custom-order products or services and goods for resale.

Best hands-off solution

Bench Accounting

Bench is a done-for-you bookkeeping service that offers the same visual reporting as the rest of the software on this list, with a bonus of an expert bookkeeper to call on whenever you need it.


Bench connects with major ecommerce platforms like Shopify, BigCommerce, and even Amazon, as well as your favorite payment processors and bank accounts. You’ll gain the same accuracy as the other major players but save even more time since Bench also handles the administrative side of bookkeeping on top of importing transactions.

If you’re having a hard time keeping up with your growing business, Bench can help by taking accounting tasks off your plate. We work behind the scenes keeping your books up to date and tax-compliant, and then present your data in your clean dashboard and reports. There are no unnecessarily complex features or opportunities for accounting errors, so you can just focus on what matters—running your business.

We also back you up with expert advice whenever you need it, so you can make sense of the reports you’re seeing and make better business decisions. If you’d rather leave your bookkeeping to the experts, Bench might be your best bet.


This additional support does come at a cost, but if you’re spending hours trying to reconcile your books on your own, that cost might be worth it. Remember, your time is worth a lot to your growing business.

Learn more: How Much Does a Bookkeeper Cost?


Bench has two primary pricing plans, with some optional add-ons depending on your bookkeeping needs:

  • Essential: $299/month
  • Premium: $499/month
  • Historical bookkeeping: +$299/month
  • Specialized bookkeeping: +$100/month

Who Bench is best for

Bench is best for small businesses and startups who want a completely hands-off approach to bookkeeping. If you’re okay paying a little more in exchange for the freedom to focus the parts of your business you enjoy, Bench might be a good fit for you.

How to choose the best ecommerce accounting software for your business

So how do you decide which ecommerce accounting software is best for your business?

Start by considering some of these questions:

  • Which features are most important to meet your business needs?
  • How important is ease of use?
  • How much experience do you have with bookkeeping?
  • How much is your time worth to your business?
  • Do you sell mostly products or services?
  • Do you sell in a few or many different states?
  • Would direct access to experts help you make wiser business decisions?

Your answers to these questions can help you start to rule out options until you’ve narrowed it down to just two or three contenders. Then, decide on the most crucial feature for you. For example, does direct integration with your ecommerce platform rank highest? Or do you need to save as much money as possible?

Present needs are important, of course, but don’t forget to keep the future of your business in mind. You’ll want to choose an accounting system you can grow with, as after you’ve put in the initial effort, you may not want to switch systems anytime soon.

How Bench can help

We might be biased, but we would recommend Bench as the best accounting software for ecommerce entrepreneurs because we tick all the boxes.

Your Bench bookkeeper imports your bank and credit card transactions to completely automate your bookkeeping, so you don’t have to do any manual data entry. As a result, you’ll save time and get the most accurate financials. When you have a bookkeeping team that stays on top of your numbers for you, you never have to worry that you’ve misclassified a transaction. Bookkeeping (and accounting) just work better with Bench.

Ready to choose the right business accounting software for your online store?

Now that you know more about bookkeeping solutions for ecommerce, take what you’ve learned and evaluate which option fits your business best. Once you’ve made your choice, set up all your integrations, and automated as much as you can—relax. Let your bookkeeping software do the heavy lifting while you mind your online business.

This post is to be used for informational purposes only and does not constitute legal, business, or tax advice. Each person should consult his or her own attorney, business advisor, or tax advisor with respect to matters referenced in this post. Bench assumes no liability for actions taken in reliance upon the information contained herein.
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