10 Best Accounting Software for Ecommerce Business

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You should be aware that no one accounting software is the best for ecommerce. It can be difficult to choose the right accounting software solution among the many available. A small business might not choose an expensive solution to send invoices as it can severely impact their profit margins.

When choosing an accounting software solution for ecommerce businesses, it is important to weigh the pros and cons. You will need basic features like invoicing, inventory management and credit card charging. Sales tax incorporation is also essential.

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Your ecommerce site will lose a lot of potential revenue if it doesn’t make it easy to pay your clients. There are many integrated solutions you have to choose from.

Some software solutions are more popular because of their pricing and feature set. These are the top accounting software options for ecommerce store operators.

QuickBooks Online

Intuit QuickBooks is a popular accounting software solution for small business owners. QuickBooks is a small business-oriented accounting software solution. It offers everything you need, including Shopify integration and an online dashboard that provides a complete overview of your company’s financial situation. QuickBooks Payments can also be used as a payment processor.

QuickBooks Online is easy to use. This is why so many businesses choose it. The program will ask you some questions about your business when you sign up. The program uses your answers to quickly create a profile and adjust core settings to optimize the program for your business type.

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It is possible to import your accounting data in Excel or CSV files. This includes all of your product, vendor and associated profiles. This is not an easy task and may require the assistance of an accountant.

The QuickBooks Dashboard provides a quick overview of your account balances including receivables and payables as well as expenses and sales. You can also access quick links to invoicing and basic maintenance.

QuickBooks is designed for entrepreneurs who have little or no accounting experience. There is a steep learning curve. You can also access important information in real time, such as bank account balances and cash flow data.

QuickBooks offers a variety of analytical and reporting tools that can be used to gain a better understanding of your store’s financial performance. Multi-channel sales data can be viewed, as well as detailed vendor and supplier records. You can also access individual templates for inventory or non-inventory parts.

You can also use it as an inventory management tool, where you can input your initial inventory. QuickBooks will then track your inventory and notify you if it falls below a certain limit.


Quickbooks has very affordable plans that make it an affordable accounting solution for ecommerce shops. Prices start at $8 per month if paid annually and reach $17 per month for the Plus package. Contact their support for additional subscriptions.

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Supports many integrations and add-ons

Framework for reporting that is highly customizable

It is easy to set up

Great support for payroll

Hybrid sales tax calculation


The customer support is not the best

The mobile app’s functionality is limited

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New users may find Dashboard a little overwhelming


FreshBooks, another great accounting system, does all the work of a digital bookkeeper. This software is ideal for ecommerce platforms who require an all-in-one solution. It is not only for ecommerce platforms; freelancers, self employed professionals and businesses with contractors can also benefit from its many features.

FreshBooks supports double entry accounting so that you don’t need to worry about creating suspense account at the end. FreshBooks also provides valuable business data and insights to help you make informed decisions about your ecommerce company.

FreshBooks began as an invoicing system. However, the company added new features and eventually became an ecommerce accounting software. It is extremely popular with startups and sole proprietors due to its affordable pricing.

Automated bank reconciliation is one of the most impressive features of the program. Automated bank reconciliations are made easier by the program’s ability to automatically import financial transactions and categorize them.

The Credits feature automates prepayments, credit notes, overpayments and credit notes. You can also access a variety of financial reports from the dashboard, such as cash flow movements and P & L.

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Inventory tracking is also possible, as well as third-party payment processors such PayPal.


FreshBooks’ popularity is due to its affordable pricing. The Lite package costs $6 per month, while the most expensive version is $20 per month and allows unlimited billing clients. They also offer custom packages for enterprise requirements.


Very simple UI

Many integrations

Functionality to make estimates and retainers

Tracking expense and mileage automatically

It integrates well with online marketplaces such as Amazon and Etsy


Quarterly tax calculations are not possible

The mobile app’s functionality is severely limited

Invoices cannot be fully customized


Then, there’s Xero. Xero is widely regarded as a flexible accounting program, which can be used by freelancers or owners of online businesses. It offers simplified functionality and affordable pricing.

It has mobile apps for iOS and Android. This makes it a great choice for those who have multiple accounting tools but want everything to be under one roof. Xero provides a great dashboard for online store owners that allows you to see a complete overview of your total spending.

Xero makes accounting easy by putting everything at one click, from balance sheets to P & L reporting. It integrates with popular platforms such as Stripe and utilizes double-entry bookkeeping.

One of the greatest things about Xero has been the constant additions to the platform over the past year, such as inventory tracking and expense management.

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It integrates well with Bigcommerce platforms for the tracking of bank transactions, and other accounting tasks. Xero Accounting may be the right tool for you if you sell on platforms like eBay.

Xero Projects is another great option for freelancers looking for time tracking. Xero is the best option if your ecommerce business is focused upon maximising profitability.


Xero is a bit higher priced than other options. The Starter package starts at $20/month, followed by the Standard ($30), and then the Premium ($40), which unlocks all functionality. Xero offers a 30-day free trial, which allows you to decide if the package is right for you.


Extensive customization features

Tracking options for projects

Reconciliation options for banks

Mobile access

Reduces time-consuming tasks such as preparing reports


You can’t set reorder levels

There is a huge difference between mobile and online dashboards in terms of features

Support via phone or live chat is limited

Wave Accounting

Wave is an ideal small business accounting solution for ecommerce store owners. Wave is an excellent choice if you are looking for a complete solution to simplify your financial accounting, tax returns and invoicing.

This accounting software is ideal for entrepreneurs who want to have complete control over their finances. You can track your payroll, invoicing and prepayments via a central portal.

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Wave makes it easy to create professional invoices for no additional cost. It also syncs with your WooCommerce store or Shopify store very efficiently. Wave offers two distinct product options: the accounting software and invoicing.

Wave makes it easy to calculate your tax due and gives you details about deferred or income tax liabilities. Wave is an accountant-friendly cloud tool that tracks your income and expenditures.

You don’t have to worry about financial information being hacked or stolen because it uses 256-bit encryption. Double-entry accounting is used, just like other programs on this list. This makes it easier for accountants to track payments through it.


Wave Accounting is completely free! Wave Accounting has no setup fees, hidden charges or recurring fees that you need to worry about. You can also make unlimited credit and bank card transactions. Wave provides unparalleled value for no additional cost. However, you will need to pay for payroll and payments.


Use it free of charge

Uses double-entry accounting

Fantastic user interface

Multiple currencies supported


Templates are very simple

The features of the mobile app are limited

Wave doesn’t allow you to offer customers discounts

The time-tracking capabilities are not available.


Kashoo, an ecommerce-centric accounting solution, automates large parts of accounting tasks for smaller businesses. It categorizes and sorts transactions automatically, which can help you save a lot of time and money.

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Kashoo has a Smart Inbox that automatically tracks vendors you do business with and prioritizes their emails. Kashoo’s mobile application uses OCR technology to scan receipts and create digital copies. The app then automatically categorizes them.

This is crucial because it eliminates the possibility of duplicate entries in your system. Kashoo automatically categorizes payments from accounts that are mainly checked by the IRS or the CRA so you don’t have worry about overpaying when the taxman calls.

Kashoo also offers a great feature: it automatically creates contacts to each invoice recipient. This saves you time and eliminates the need to manually enter or import data.

Kashoo makes online payments and transactions easier by allowing users the ability to accept payments from multiple sources. It is powered by WePay and greatly reduces the friction of payment. Kashoo is a great choice for SaaS businesses.


They offer a $0 per month free service for small businesses. The accounting package costs $20 per month and the complete offering is $30. However, the free option is only for invoicing.


Constant updates

Decent for expense and income tracking

Smaller businesses get a free version

A good selection of templates


There is no traditional dashboard. Everything is divided by tabs

Android app still in development

Very limited number of integrations

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Zoho Books

All types of businesses can benefit from the Zoho suite software programs. A variety of productivity apps are available for business owners and marketers. As you can see, Zoho Books is a financial service offering that targets small businesses.

Zoho Books is a great choice for small business accounting. Zoho Books is extremely easy to integrate into ecommerce platforms for those who already use Zoho.

It provides convenient features for payroll management, billing, invoice, billing, making estimates and expense tracking. Zoho Books is a great choice if you are looking to automate your accounting department’s workflows.

Zoho Books provides an integrated accounting solution that tracks sales orders and deals. You can also get a clear view of your business’s performance with Zoho Books’ reporting tools.


Zoho Books is available for businesses that generate less than $50k annually. The Standard plan costs $10/month and there are two additional options at $20 and $30 per months. Additional branches and users can also purchase add-ons.


All major payment gateways supported

Time tracking

Their support services are renowned in the business sector.

Features include form management and customization


Payroll features are not offered globally or in all countries.

There are few integration options.

Sage Accounting

Sage Accounting is last but not least. Sage Accounting is one of the most feature-rich options available. Sage is a major player in cloud accounting solutions.

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Sage is very easy to use if you’re an accountant. Sage can seem like an application that is geared more towards accountants than small business owners.

You won’t find certain features in Sage that you don’t normally find in other programs like time tracking and managing purchase orders. Sage provides a number of signup tools to help you quickly set up Sales and Expense options as well as tax returns.

It is easy to use and has double-entry bookkeeping, which is a big win for accountants. Sage’s interface is a bit outdated compared to other big brands like Zoho Books and QuickBooks. This will be something that many people will notice.

Sage also offers mobile apps for Android and iOS. Both are well-designed. You can also import CSV files that support multiple types of data.


Sage offers 70% discount for the first six months. The Sage Accounting package is $25 per month and the Start package is $10 per month. For the first six months, the Sage Accounting package is $7.5 per monthly.


It is very easy to set-up

Simple interface

Offers project tracking options

Apps for Android and iOS that are decently designed are available.


It looks old.

No time tracking

Report customization is limited

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What is Ecommerce Accounting Software?

Ecommerce store owners require robust software that can quickly adapt to their requirements. An accounting program that tracks inventory, vendor payments, sales, and more is essential for ecommerce store owners.

It is important to deploy a software program because ecommerce websites are largely automated. This will ensure that all transactions are recorded. You need to choose an accounting program that offers flexibility and has a lot of variable costs.

Ecommerce accounting software makes it easy for store owners to keep track of all transactions in their store. This software program will allow store owners to monitor inventory levels, calculate their profit margins and other details such as tax payables, accounts receivables, overhead expenditure, and more.

Cloud-based accounting software means that you don’t need to install or save data on your computer. You can also access your records from any device. All you have to do is log in to the account to view the most recent figures.

Nearly every ecommerce accounting solution offers a range of solutions that can be customized to suit your needs, from simple invoicing to customizable reports. The software should generate an invoice for every purchase.

These software programs can also be used to track suppliers. They can issue receipts to suppliers, and update inventory records.

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How to Choose an Accounting Software For Ecommerce Businesses

There are many options for those looking for an accounting software that will work well for ecommerce businesses. If you know exactly what you want, however, it is possible to narrow down your options. These are the key features that ecommerce store owners should look out for in an accounting software.


You should choose a program that can generate different reports with just a click. This includes basic financial statements such as the statement on financial position, statement of profit or loss, and statement regarding cash flows.

The program should also offer extensive data visualization options. Users should be able to use the program to create bar graphs and pie charts, as well as other visualizations to help them see the state of their stores.


All your sensitive data should be protected by the software program. The ideal accounting software solution should have 256-bit encryption and two-factor authentication so that authorized personnel can access the dashboard. Most business owners are concerned about security, particularly since all sensitive information is stored in cloud.

Anyone with some technical knowledge and the ability to use brute force tools, can hack into any software program that lacks security.


You will also want an accounting program that seamlessly integrates with any other programs installed on your store. If your store is built on Shopify, then the accounting software program must seamlessly integrate to track payments as well as invoices.

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Most major software programs offer integrations and add-ons to increase functionality. This makes it possible for you manage your store from a single platform. Collaboration is essential between departments like inventory and payroll.

Get prompt support and the latest information

You should ensure that the program you select has regular updates and support. To improve the program’s performance, the team should be active in adding new features to it.

They should take customer support very seriously. If you have any questions, there should be multiple options for support, including email, phone, and live chat. This gives the user confidence and shows that they care about the product.

The bottom line

It is crucial to use an accounting shop for ecommerce store owners. It’s not a good idea to scramble at the last moment when taxes are due. It is a good idea to have all the reports you need available at any given time. You can do this with a good accounting software program. Choose from these seven options!