Around 64% of small businesses use accounting software. Yet, it can be challenging for online sellers to determine the best accounting software for ecommerce.

Businesses use accounting software to track sales, reconcile accounts, invoice customers, and stay tax compliant. So, what should ecommerce sellers look for when deciding on the best software for the job? Below, we’ll review eight top picks, including key features and pricing.

What is ecommerce accounting software?

Ecommerce accounting software helps businesses manage their financial transactions and records. Accountants and bookkeepers use it to track income and expenses, create invoices, manage inventory, and generate financial reports.

Whether it’s bookkeeping or accounting tasks, online sellers benefit in the long run by maintaining accurate financial records that meet sales tax and business compliance regulations. Overall, accounting software helps streamline operations and ensure financial health. 

Best ecommerce accounting software features

Every ecommerce business has unique needs, and not all software is created equal. Consider the following key features when deciding which tool suits your business.

Ecommerce platform integrations

When it comes to ecommerce platforms, seamless integrations make all the difference for financial management. Online sellers need software that syncs data from their online storefront to their accounting system, including order details or customer information.

Point of sale and payment processing integrations

Accounting software should streamline payment processing and reduce accounting workload. Online sellers should also consider whether or not their POS system integrates with their accounting solution of choice.

Streamlining systems can give you more time to focus on growth and customer satisfaction instead of manual record-keeping.

Sales tax compliance capabilities

Tax laws are already complex and constantly changing. Sellers not only need to understand ecommerce sales tax compliance, but they also need to know when and how often to remit to avoid penalties.

Their chosen accounting solution should offer robust tax reporting and compliance tools to keep them ahead of the curve and worry-free. 

Top accounting software for ecommerce business owners

Once you’ve identified the key software features, it’s time to explore the various options to determine the best fit for your business. Take a look at our list of popular ecommerce accounting solutions.

QuickBooks Online

When it comes to familiarity, QuickBooks Online reigns supreme. Arguably, as the most widely used accounting software, QuickBooks covers nearly every base most businesses look for in financial management.

QuickBooks Online works best for small to mid-sized businesses that prefer cloud-based accounting software. There are plenty of reasons to weigh QuickBooks Online vs. QuickBooks Desktop. But, generally, more experienced accountants and bookkeepers may want the desktop software for its more advanced accounting features.



  • Simple Start: $15
  • Plus: $45
  • Advanced: $100


Unlike others on the list, Oracle’s NetSuite is an enterprise resource planning system (ERP), accounting being one of the many tools included. Businesses can streamline their accounting tasks and expand their efforts across their entire operation.

NetSuite works best for online sellers who want flexibility when scaling their businesses. With its customization options and a suite of applications, ecommerce sellers can focus on growth while NetSuite handles the rest.


  • Advanced customization
  • Industry-specific apps
  • Built-in reporting tools
  • Inventory, order, and tax management


  • Varies based on business size


OneUp distinguishes itself by focusing on mobile friendliness, though it doesn’t neglect its browser-based interface. It offers comprehensive customer relationship management tools, making it ideal for those who prioritize customer retention.

OneUp functions best for businesses seeking inexpensive solutions that fit in their pockets. The ability to easily categorize transactions and generate purchase orders makes it a viable solution for budget-minded sellers.


  • Mobile app
  • Automatic transaction categorization
  • Automatically generate purchase orders when stock is low
  • Customer relationship management tools


  • Self: $9
  • Pro: $19
  • Plus: $29
  • Team: $69
  • Unlimited: $169

Zoho Books

Zoho Books is one of many applications under the Zoho brand, the others being inventory, invoicing, and customer relationship management solutions. It also offers a free plan, making it one of the more affordable business options.

Zoho Books appeals to ecommerce owners who want to try an accounting software system they can use alongside other operational tools. It also offers 24-hour live chat support Monday through Friday.


  • Free plan available
  • Live chat support
  • Inventory and invoice management
  • Workflow rules for transactions


  • Standard: $15
  • Professional: $40
  • Premium: $60
  • Elite: $120
  • Ultimate: $240


Wave is for the entrepreneur on the go. Its mobile app allows online sellers to manage their finances easily and includes customizable sales tax and invoice statuses.

Wave is an accounting solution for freelancers and independent contractors who need simple and affordable software. And it offers a free plan with impressive income and expense tracking features.


  • Free plan available
  • Unlimited income and expense tracking
  • Customizable templates
  • Send invoices from the mobile app


  • Starter: $0
  • Pro: $16


Sage's mission is to serve businesses of all sizes, whether theirs is a well-established corporation or a brand-new freelance business. It also opts to keep things simple by focusing on the basics of financial management.

Sage functions best for ecommerce business owners who don’t need anything outside of core accounting functions. Its bank reconciliation and workflow solutions, in particular, help it attract businesses seeking robust yet affordable features.


  • Provides audit trails
  • Accommodates multiple companies
  • Streamlined bank reconciliation
  • Order process workflow


  • Pro: $59
  • Premium: $97
  • Quantum: $160


Freshbooks is another product that simplifies things for its users. The mobile app allows ecommerce business owners to generate invoices, scan receipts, and track mileage, making it another great option for entrepreneurs on the go.

Freshbooks works best for freelancers and independent contractors who need a simple, affordable tool for organizing their finances. It also integrates with over 100 third-party apps and offers phone support throughout the workweek.


  • Send invoices, scan receipts, and track mileage via mobile app
  • Integrates with over 100 third-party apps
  • Phone support Monday through Friday
  • Inventory and billable items tracking


  • Lite: $19
  • Plus: $33
  • Premium: $168


ZarMoney excels at inventory management, a crucial aspect of ecommerce operations. In addition, it offers specialized training for new users and a dedicated account representative.

ZarMoney works best for businesses needing comprehensive inventory management tools. It also functions similarly to an ERP, meaning it’s a great choice for businesses seeking a low-cost tool for operational oversight.


  • Multisite inventory management
  • Split transactions
  • Real-time inventory data
  • Customer payment reminders


  • Entrepreneur: $15
  • Small Business: $20
  • Enterprise: $350

Choosing the best accounting software for your business

Ultimately, the best accounting software will depend on the individual needs of your business. So consider the following factors when choosing accounting software.

Your business needs and budget

List any essential features your business needs vs. those you can manage without, along with a realistic budget. Doing so can help you narrow down your options so you’re not paying for features you won’t use.

For example, a freelancer just starting out may benefit from a free plan that only includes core features. Likewise, an established ecommerce shop may need an advanced plan that’s easily scalable.

Your user-friendliness and scalability needs

Just as you want your site to be easy for your customers to navigate, the same should apply to your accounting software. Aim for an intuitive interface and a responsive support network in case you need help troubleshooting.

As your business grows, your accounting software should be able to keep up and offer advanced features.

Security and customer support availability

Prioritize software with strong security measures in place to protect sensitive customer information. These measures should also include customer support, the ability to get help on your own, and clear instructions for contacting a representative.

Reviews, recommendations, and success stories

Read software reviews carefully to ensure a good fit. It also never hurts to search online forums and ask other entrepreneurs what works for them. Additionally, word-of-mouth still goes a long way. Connect with business owners in your industry or niche for recommendations.

Finally, real-world examples go a long way in providing context and practical use for a particular industry. Explore examples of other businesses using the software and consider whether it would apply to your environment.

Automate your daily work to stay on top of your business

No matter what ecommerce accounting software you choose, you're going to experience a fair amount of data entry in your day-to-day life.

Unfortunately, doing everything by hand — adding orders, updating price and GOGS data, reconciling, etc. — can be time-consuming and lead to costly accounting errors down the line.

But you can pair your accounting solution with an ecommerce automation tool to mitigate risks and save time. Automation can seamlessly connect QuickBooks Online or QuickBooks Desktop to your marketplace apps, online storefronts, shipping platforms, and more so you can sync transactions as they occur. In fact, real-time automation has saved 70% of sellers up to 10 hours per week on manual processes.

At the end of the day, knowing who the major players are in ecommerce accounting software and how to make that software work better for you can set you down the most effective path to ecommerce growth and long-term success.