Top 7 Ecommerce Accounting Software

Top 7 Ecommerce Accounting Software

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Every ecommerce accounting software solution promises to save you time and improve your business, so which should you choose?

At POP Business, we’ve set up many clients with the right tools for their ecommerce accounting needs. We can tell you from experience – it’s all about finding the right fit.

Because every ecommerce business is different, we’ve put together a list of seven top applications and the types of organisations they’re likely to suit.

Ecommerce Accounting Software for the Australian Market


Thriday, a next-generation accounting platform, is tailored for small business owners seeking efficiency and cost-effectiveness. Thriday uses AI to automate tax calculations and identify eligible deductions, providing a seamless and hassle-free financial management experience. You can join Thriday for free, and its premium package is only $29.95 a month.


Xero is a cloud-based ecommerce accounting software that will work well for most small businesses.

You can send online invoices and quotes, sync bank reconciliations, track bills and store receipts electronically.

Xero accounting software logo

The standard plan includes payroll for two people. You’ll need to upgrade to a premium plan to cater for more employees and automate superannuation calculations.

Xero connects to a time-tracking app to support billing by time. It includes inventory management software for retailers too, so you can monitor stock levels and identify popular items.

Strong on the tax front, Xero makes income tax preparation and BAS reporting a breeze.

Price-wise, you’ve got flexibility with Starter, Standard and Premium plans with optional add-ons for each. All plans include multiple users, automatic software updates and on-the-go accessibility.

You can even opt for a payroll-only plan if that’s all you need.


A household name, MYOB potentially suits those looking to work both online and offline.

MYOB ecommerce accounting software Logo

MYOB ecommerce accounting software offers two products – Essentials and AccountRight. Essentials is online-only and offers on-the-go flexibility. AccountRight allows you to work online or offline but isn’t accessible from your mobile phone. You can choose either a starter, standard or premium plan with each product. Payroll-only plans are available as well.

Both Essentials and AccountRight will help with managing cashflow, sending invoices and quotes, and tracking jobs. They’ll calculate GST and lodge your BAS electronically. Both offer BPAY and card payments.

However, if you want to keep track of customers, suppliers and inventory, or to bill customers by time, you’ll need a subscription to an AccountRight plan – which are pricier than Essentials plans.

QuickBooks Online

QuickBooks offers Simple Start, Essentials and Plus plans, as well as an alternative for self-employed individuals. Its highly competitive prices are a true stand-out.

Small businesses will benefit from tools to keep an eye on income and expenses, send unlimited invoices, and snap and store receipts. All plans come with GST tracking, BAS reporting and lodgement, automatic updates, and secure cloud storage.

QuickBooks ecommerce accounting software logo

You’ll need a standard plan subscription for multiple currencies and to schedule recurring bills. Inventory tracking is only available on a premium plan.

Though a cheaper alternative, there are two major considerations with QuickBooks ecommerce accounting software you should be aware of.

Firstly, you can only manage a maximum of five users on the QuickBooks premium plan (three users if you’re on a standard plan). This could be a problem if you want to grant access to select employees.

Secondly, payroll is an optional add-on priced on a per employee per month basis. This could get expensive as your payroll grows.

Sage Business Cloud Accounting

Sage dispenses with tiered pricing and charges $20 per month, GST-included. Its simplicity will appeal to small business owners worried about potential hidden costs with tiered plans.

Sage’s ecommerce accounting software features payroll for up to four employees, access for up to two users, automated bank feeds, electronic invoicing, BAS reporting, supplier and customer management, intelligence reporting and a range of mobile apps so you can run your business from anywhere. Cashflow forecasting is included too. You’ve also got unlimited transactions and bank and credit card processing.

But you’ll have to pay extra for direct bank feeds, time tracking, use of multiple currencies, additional employees for payroll or access for more users.


Marketing itself as the Australian version of FreshBooks, Rounded will appeal to freelancers or sole traders who want a local product billed in Australian dollars.

Rounded ecommerce accounting software logo

Unlike FreshBooks, Rounded offers unlimited invoices, quotes and client management on both its Starter and Pro plans. You can track time and expenses, accept credit payments and schedule recurring invoices too.

However, you’ll need to be on the Pro plan to track GST, lodge your BAS and connect to your bank account.

Other Ecommerce Accounting Software


FreshBooks isn’t tailored to the local market so working out your taxes won’t be as easy.

While basic inventory monitoring is available, FreshBooks is geared toward managing clients and billing as a freelancer or sole trader.

freshbooks logo

It’s got standard features you’d expect like invoice creation, payment acceptance, expense tracking, billable time tracking and financial reporting.

But tools to improve client relationships is where FreshBooks e-commerce accounting software shines. You’ve got multi-language invoices and internal client notes where you can create and store information about each client. You can also prepare attractive proposals and easily convert estimates or quotes into invoices.

There are Lite, Plus and Premium plans, and a custom plan for businesses with more complex needs. The Lite plan allows you to send unlimited invoices to a maximum of 5 clients.

Apart from taxes, another potential downside is that you’ll need to pay per team member to give them account access.


ZipBooks is an ecommerce accounting software with an enticing difference – it offers a free plan as well as tiered pricing.

Zipbooks logo

The free plan allows you to send unlimited invoices, manage unlimited vendors and customers, and accept digital payments. You can also connect to one bank account and view basic reports.

This level of features for zero cost is likely to appeal to startups or owners who are unfamiliar with ecommerce accounting software, and prefer to dip their toes in before making a commitment.

But you’ll probably need to upgrade to a paid plan in the long run. As your business grows, you’ll benefit from features like additional team member access, scheduling recurring invoices, time tracking and payroll integration – which are only available on paid plans.

Like FreshBooks, ZipBooks wasn’t designed with Australian taxes in mind and you’ll be charged in US dollars. There’s no inventory tracking either.

Eccomerce Accounting Software Summary

Hopefully, one thing has been made clear – ecommerce accounting software packages are all different. So what suits one business might not work well for another.

If you need a hand to choose the right product, contact POP Business. We’re cloud-based tax accountant specialists and we’re proudly tech-driven. Whether it’s to connect your accounting software, streamline processes, or to optimise your tax position, we can help you take your businesses to the next level.

At POP Business, we’re also a Xero Platinum Partner which means we can get you set up on Xero quickly and easily.  What’s more, we can provide you with a 20% discount on your subscription.

Call us today on 1300 180 630!

Picture of Sidney Cachuela

Sidney Cachuela

I am a business mentor, an associate financial advisor and one of the co-founders at POP that genuinely revels in solving complex problems that businesses face. I’ve worked with high profile wealth managers, financial advisors and business owners to drive innovation and achieve success. My expertise includes helping small businesses with a range of accounting services, including: financial advice, accounting and bookkeeping, GST tax planning, as well as company, trust and partnership tax returns and more.

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