Introduction
Running an ecommerce business is thrilling — until it’s time to deal with the numbers. Managing sales, expenses, VAT, and cash flow manually can quickly turn into a stressful and time-consuming task. That’s where the right accounting software comes in.
But with so many options on the market, how do you choose the best one for your ecommerce store? In this blog, we’ll review the top accounting software platforms tailored for online businesses, sharing expert insights to help you stay organised, compliant, and profitable. Whether you’re just starting out or scaling fast, we’ve got you covered.
Why Ecommerce Businesses Need Specialised Accounting Software
Ecommerce businesses have unique accounting needs. You’re often dealing with:
- Multiple sales channels (Amazon, Shopify, Etsy, WooCommerce).
- International customers and currencies.
- Complex VAT rules, especially UK VAT for online sellers.
- Inventory management and shipping costs.
Generic bookkeeping tools might not handle all of this smoothly. Choosing accounting software that integrates with your ecommerce platform — and supports efficient business tax filing online — can save you hours of work and reduce costly errors.
👉 Need help setting up or managing your ecommerce finances? Explore our Ecommerce Accounting Services.
Top 5 Accounting Software for Ecommerce Businesses
1. Xero
Xero is a favourite among ecommerce business owners — and for good reason.
Pros:
- Seamlessly integrates with Shopify, Amazon, Etsy, and more.
- Automates bank feeds, invoicing, and VAT calculations.
- Great for multi-currency businesses.
- Easy to use, even if you’re not a numbers person.
Cons:
- Some ecommerce integrations require paid third-party apps.
Expert Verdict: If you want simple, scalable accounting with powerful reporting, Xero is an excellent choice.
2. QuickBooks Online
QuickBooks is another heavy hitter in the ecommerce accounting world.
Pros:
- Strong inventory tracking features.
- Direct integrations with Amazon and Shopify.
- Automated sales tax/VAT features.
- Comprehensive cash flow forecasting tools.
Cons:
- Slightly steeper learning curve for beginners.
Expert Verdict: Ideal if you have complex inventory needs or plan to scale quickly across multiple sales channels.
3. A2X
A2X isn’t a full accounting software on its own — it’s a powerful add-on designed specifically for ecommerce sellers.
Pros:
- Accurately reconciles Amazon, Shopify, and eBay sales with your accounting software.
- Handles complicated fee structures automatically.
- Essential for clean, audit-proof records.
Cons:
- Requires linking with Xero or QuickBooks.
Expert Verdict: Essential for serious sellers handling high transaction volumes who want flawless bookkeeping.
4. Sage Business Cloud Accounting
Sage offers an affordable, straightforward solution for smaller ecommerce businesses.
Pros:
- Easy to use for new business owners.
- Built-in VAT management.
- Strong customer support based in the UK.
Cons:
- Limited ecommerce integrations compared to Xero or QuickBooks.
Expert Verdict: A good starter option if you’re running a single online store and need a simple, budget-friendly system.
5. FreeAgent
Tailored for small businesses and freelancers, FreeAgent can suit solopreneur ecommerce stores.
Pros:
- Very user-friendly interface.
- Automatic expense tracking and invoicing.
- Designed with HMRC compliance in mind.
Cons:
- Not ideal for complex inventory needs.
Expert Verdict: Best suited for small, service-based ecommerce sellers who prioritise simplicity over deep functionality.
Choosing the Right Software for Your Ecommerce Business
When deciding which tool is right for you, consider:
- Size and complexity of your business: High transaction volumes and multiple platforms demand robust software like Xero or QuickBooks.
- VAT requirements: Make sure your software can handle UK VAT for online sellers if you’re registered.
- Budget: Weigh the software cost against the time and error savings it provides.
- Integration capabilities: Ensure your sales channels and payment gateways integrate smoothly.
An experienced accountant offering ecommerce accounting services can recommend and even help implement the best system for your needs.
👉 See how we support ecommerce businesses with Business Tax Services.
Conclusion
Choosing the right accounting software isn’t just about staying compliant — it’s about gaining better control over your ecommerce business and freeing up time to focus on growth. Whether you choose Xero, QuickBooks, or another platform, the right system will make business tax filing online faster, easier, and less stressful.
Need expert advice on setting up your accounting software or managing your ecommerce finances? Book a free consultation with Centralyze Accounting today — let’s build a financial system that grows with your business!