Ecommerce Accounting Software

With the best ecommerce accounting software and your very own custom financial dashboard you’ll start to see how your online store is really performing!

ecommerce accounting software

What Is Ecommerce Accounting Software

Ecommerce accounting software is a specialized tool designed to handle the unique accounting and bookkeeping needs of online businesses. It streamlines bookkeeping, tax calculations, inventory management, and financial reporting, allowing ecommerce entrepreneurs like you to focus more on growing your online business.

Who Needs Ecommerce Accounting Software & Why

Every ecommerce business, regardless of its size or industry, can benefit from ecommerce accounting software. 

Having trouble tracking inventory movements or profitability per sales channel? 

Getting your sales tax calculations wrong? 

Specialized accounting software for ecommerce will help!  Without it, managing the financial aspects of your online business can be overwhelming and prone to errors.

Who needs ecommerce accounting software

Our Very Own Ecommerce Accounting Software

At HiroCFO, we have put together the best accounting software for ecommerce. 

Our specialized team of ecommerce accountants have custom-built a financial dashboard that integrates with your online store, accounting software, and the bookkeeping applications and tools you utilize.

All of your financial data is pulled into one central place. From there, we give you one clear dashboard that provides you with all of your key performance indicators.

Key Features Of Our Dashboard

Our custom reporting platform is made up a number of dashboards that will show you real-time graphics and visuals on KPIs like:

Revenue v expense v profit

Operating cash flow

Cost of goods sold (COGS)

Most profitable products

Inventory insights

Outstanding receivables

Expense dashboard

Top 10 expenses

Top vendors

Sales & income tax

Net assets

Real revenue

P&L statement

It’s one simple and clear place to visualize all of the key financial information in your ecommerce business. Plus, you’ll also be able to track all the bookkeeping & accounting tasks that our ecommerce accountants are taking care of for you, month by month.

Ecommerce Accounting Software Pricing

Our custom built financial dashboard is included for free as a value-add to our ecommerce bookkeeping services. Book a free demonstration of the dashboard today!

Pricing for ecommerce accounting software

How It Works

Once you sign up with HiroCFO, we work with you to understand your business needs and KPIs. We then build a custom dashboard that integrates seamlessly with your accounting and bookkeeping data. You can log in anytime to access your financial data and make better business decisions.

How ecommerce accounting software works

Customer Reviews

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Brian F

Colin and his team have been doing my books and tax planning for months and have done an excellent job!

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Emma C

Hiro cleaned up my books and gave me a better understanding of my company’s finances than I ever thought possible!

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Jessica M

I run an e-commerce store and know nothing about accounting. Their financial dashboards have helped me understand all my finances. Highly recommend!

7 Of The Best Ecommerce Software Platforms

There are numerous ecommerce accounting software options available in the market. Here are 7 of the top ones:

QuickBooks Online

QuickBooks Online is our choice for the best overall ecommerce accounting software because of its integration opportunities and inventory features.

Key Features
Direct integrations with Shopify, WooCommerce, Magento, and BigCommerce. Connects with additional ecommerce apps through Webgility, A2X, Connex, and Parex Bridge. It automatically applies sales tax based on transaction location and files sales tax returns.

Much cheaper than QuickBooks and includes unlimited users in all plans.

Must manually set up sales tax rates for each location with a taxable sale. Cannot file sales tax returns.


QuickBooks Online

Quickbooks ecommerce accounting software

Ranges from $30 per month for one user to $200 per month for 20 users.


Zero ecommerce accounting software

All Xero plans include unlimited users and range from $13 to $70 per month.


Xero rivals QuickBooks Online in inventory, accounts receivable and accounts payable management. However, Xero really stands out in project accounting and fixed asset management and wins over QuickBooks in the fact that it can accommodate an unlimited number of users.

Key Features Direct integration with Shopify. Integrate with third-party connectors A2X, and Parex Bridge. Good inventory accounting.

Pros Much cheaper than QuickBooks and includes unlimited users in all plans.

Cons Must manually set up sales tax rates for each location with a taxable sale. Cannot file sales tax returns.

Zoho Books

Zoho Books is one of the apps included within the Zoho suite of small business management products. When choosing Zoho Books, you get a seamless integration with more than 40 other Zoho applications that can manage your entire business.

Key Features Integrates with other Zoho apps to provide a complete suite of management software. Integrates with many ecommerce apps through Zoho Flows, which requires a separate subscription.

Pros Good basic accounting features. Integrates with other Zoho apps to provide a complete suite of management software.

Cons No ecommerce integrations without subscribing to either Zoho Inventory or Zoho Flows. Cannot determine sales tax rate by location or file sales tax returns.

Zoho Books

Zoho ecommerce accounting software

Ranges from $0 to $275 per month depending on the plan.


Wave ecommerce accounting software

Free for accounting and invoicing.


Wave is a free accounting software. You can send unlimited invoices to customers, set up unlimited companies, and keep track of your accounts at no cost.

Key Features Free forever. Integrates with Zapier. Good basic accounting features.

Pros Free for accounting and invoicing. Integrates with Zapier.

Cons No direct ecommerce integrations or third-party connectors. Limited inventory accounting. Cannot determine sales tax rate by location or file sales tax returns.


FreshBooks is an accounting software platform that is especially popular with small businesses. It offers a range of features including expense tracking, time tracking, and invoicing.

Key Features Easy to use interface, customizable invoices, automatic expense tracking, time tracking, and project management.

Pros User-friendly, excellent customer service, good reporting features.

Cons Limited inventory management features, no payroll services.


Freshbooks ecommerce accounting software

Plans start at $15 per month.

Sage 50Cloud

Sage 50cloud ecommerce accounting software

Plans start at $50.58 per month.

Sage 50cloud

Sage 50cloud is a comprehensive accounting solution that combines the convenience of cloud access with the power of desktop accounting software. It offers features such as invoicing, cash flow management, inventory management, taxes, and more.

Key Features Comprehensive financial management features, advanced security, Microsoft Office 365 integration.

Pros Loads of features, strong security measures, integrates with Microsoft Office 365.

Cons Can be expensive for small businesses, steep learning curve.


NetSuite is a comprehensive business management suite that includes features for ecommerce. It’s a scalable solution that can grow with your business.

Key Features Real-time visibility into the business performance, financial management, billing, and ecommerce.

Pros Comprehensive features, scalable, real-time visibility into business performance.

Cons Can be expensive for small businesses, steep learning curve.


Netsuite ecommerce accounting software

Pricing is customized based on the specific needs of the business.

Software We Integrate With

ecommerce bookkeeping software quickbooks logo
ecommerce bookkeeping software Xero logo
ecommerce bookkeeping services app A2X logo
ecommerce platform shopify logo
gusto logo
ecommerce store amazon logo
bill.com logo
stripe logo
expensify logo
tax jar logo

How to Choose the Right Accounting Software

Choosing the right ecommerce accounting software depends on several factors, including your business size, industry, budget, and specific financial needs. Consider features like real-time reporting, tax automation, inventory management, and integration with other business tools.

With HiroCFO you get all of this, plus on-going accounting support from our team of experts. 

Let’s simplify your financial systems and get you the data you need to drive your ecommerce store’s success.
Submit the form for a free demonstration of our dashboard and services.

Speak To An
Ecommerce Accountant

4613 Floyd Street Houston,
TX 77007

Contact Us

Submit the form and we’ll get back to you asap!


The best accounting software for ecommerce stores depends on the specific needs of the business. QuickBooks is a leading ecommerce accounting software.

Route accounting software is a specialized tool designed for businesses with delivery or distribution routes. It helps manage inventory, track deliveries, and handle financial transactions along specific routes.

Yes, accounting software can greatly simplify financial management for small businesses, saving time and reducing errors.

QuickBooks is user-friendly and offers a variety of tutorials and resources for new users. You can use it to track income and expenses, invoice customers, pay bills, generate reports, and prepare for taxes.

A2X is an accounting software for ecommerce specifically designed for businesses that sell on platforms like Amazon and Shopify. It automates the import of sales data and fees from these platforms into accounting software like QuickBooks or Xero.

Yes, Stripe is a secure platform for online payment processing. It complies with the highest industry standards for data security and encryption.

Yes, Stripe can integrate with QuickBooks, allowing for seamless transfer of sales data into your accounting software.

Shopify does not have its own accounting software, but it integrates with several popular accounting software platforms like QuickBooks, Xero, and A2X.

Amazon sellers often use accounting software like QuickBooks, Xero, or A2X, which can integrate with Amazon’s platform to automate sales data import.

Amazon accounting involves tracking and recording all transactions related to your Amazon sales, including sales revenue, fees, and cost of goods sold. This can be done manually, but it’s much easier and more accurate with accounting software for ecommerce.

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