How to Choose the Right Accountant for Your eCommerce Store

Introduction

eCommerce is one of the fastest growing sectors in the world, primarily in the UK. Online businesses with the evolution of mobile phones and the internet have seen a boom unlike anything in history. The pattern of online shopping has changed with masses preferring online mode of buying products and services, rather than going shop to shop in scorching heat. As the industry grows, the demand for skilled accountants for eCommerce has risen among UK businesses looking to stay financially sharp and compliant.

With such ease, running an eCommerce business has become increasingly complex having an inverted relation to development. The financial aspect of the online businesses are governed by laws, regulations and region-goverened compliances. Hence working on the financial aspect in hand with operational, is no one man task if you aim for a long-term sustainable growth. That’s why many UK online sellers now hire accountants for their eCommerce businesses. This means managing orders across platforms like Amazon and Shopify, tracking stocks, dealing with fees, and staying compliant with tax laws like UK VAT or EU OSS – is one less thing to worry about.

This guide will explain how eCommerce accountants differ from your general accountants, and why choose E2E that offers a full-suite accounting solution from just £25/month.

Understanding the Role of an eCommerce Accountant

An eCommerce accountant helps online sellers manage the complex financial side of running an online store. They automate the accounting and bookkeeping processes, and help in creation of reports and management accounts to adhere, as well as find areas of improvement and eliminate the bottlenecks.

They are not just accountants – they’re digital experts having years of experience in the eCommerce niche. Unlike your traditional accountant that offers generic accounting solutions, accountants for eCommerce deliver customised accounting as per the need and goals. Whether you are a start-up, or a well-established store, a dedicated eCommerce accountant ensures your tax liability is legally minimised, while you claim deductible expenses. They are well-versed with platform-specific accounting needs for Amazon, Shopify, eBay, and more. Here’s what they help you out with

• Track sales, fees, and refunds from Amazon, Shopify, eBay, and others
• Handle VAT (UK, IOSS, OSS) so you avoid penalties
• Sync your online store with tools like Xero, QuickBooks, and A2X
• Report profits after fees, ads, returns, and promotions
• Forecast cash flow for seasonal sales

Why Your eCommerce Business Needs a Specialist Accountant

If you are reading this blog, you’re probably in the decision stage – wondering which accounting firm to choose. Before diving into it, let’s understand the need for a specialist eCommerce accountant.

Unlike your regular store, eCommerce is your digital store that is available and accessible 24/7. Sales happen across multiple platforms- each having their own rules and fee structure. You deal with endless transactions, ever-changing VAT rules, and customers across borders. One small mistake can wipe out chunks of your profit, sending you back to where you started.

The gap in the expertise between traditional accountant and eCommerce accountant is exponentially visible. Imaging you are an Amazon seller with a sale of £50,000 in the last month. Happy right? But what if your accountant only sees the top-line revenue and file taxes based on that?

A specialist eCommerce accountant would dig deeper. They’ll break down that £50,000 like this:

• Amazon fees: £6,000
• Ad spend (PPC): £4,500
• Refunds and chargebacks: £2,000
• Shipping & fulfilment: £3,000
• VAT liabilities: £2,500

So, your actual profit? Around £32,000 or even less — depending on your other costs.

A general accountant might miss or misclassify these key deductions.A specialist, on the other hand, ensures every penny is accounted for — giving you accurate books, real profit visibility, and clear insights to grow your business. In a nutshell, specialist help to-

• Avoid missing tax deadlines or overpaying VAT
• Ensuring books are always up to date — no more late-night spreadsheets
• Knowing your real profits (after ads, shipping, returns)
• Advice on how to scale smartly and profitably

Essential Accounting Services Every Ecommerce Business Should Know About

• Bookkeeping: E2E strengthens your foundation by precise categorisation of sales, expenses, and fees, giving you clean records and clear insights into Accounts payable and receivable. Our dedicated bookkeepers automate the daily/weekly sync across different platforms, ensuring you are backed by real-time data when making business decisions.

• VAT & Tax: eCommerce VAT obligation is like a tricky puzzle, with different rules for the UK, EU (IOSS/OSS), and global sales. E2E helps you put all the pieces together by ensuring you’re registered where needed, tracking thresholds, filing returns on time, and staying compliant no matter where you sell.

• COGS & Inventory: With E2E’s 360 eCom dashboard, sellers get insight into cost of goods sold minus refunds, discounts, and hidden costs — giving a true picture of product profitability and preventing the overstocking or understocking of the inventory.

• Multi-platform Integration: Whether you sell on Amazon, eBay, Shopify or other eCommerce platforms, E2E presents data all in one place within a customisable eCom dashboard. No manual work required.

• Advisory: E2E acts as your financial co-pilot — offering support with pricing strategies, cash flow planning, budget forecasting, software selection, and long-term growth decisions. We go beyond the basic bookkeeping and accounting needs.

Popular Accounting Software for eCommerce Businesses

• QuickBooks or Xero: The most popular accounting program for small and medium sized businesses is QuickBooks and Xero, having the capability to accurately handle inventory, taxes, expenses and more. With this software, ecommerce sellers can anytime check due dates, money spent, and accounts due. It is popular in the UK for its seamless MTD compliance feature.

• A2X or Link My Books: Another UK friendly tool is A2X and Link My Books. The software directly pulls data from your eCommerce platforms – including VAT breakdowns, marketplace fees, refunds, and multi-currency transactions. If you are to choose amongst the two, consider factors like pricing, features and scalability.

• ClearBooks: Compared to QuickBooks and Xero, this software is more locally focused with a simple interface. It’s a HMRC-recognised software, offering simple VAT filing, invoicing, and bank reconciliation. If you sell on Amazon, Shopify and require advanced features like multi-currency transaction, inventory tracking, then Xero or QuickBooks will be a better fit

• Shopify, WooCommerce, and eBay Plugins: Accountants often need the support of various plugins to connect these platforms to accounting software like Xero or QuickBooks. These integrations help pull in daily sales, VAT breakdowns, shipping fees, and refunds — giving a real-time, accurate view of your store’s financials without manual data entry.

Tips for Selecting the Best Accountant for Your E commerce Business

When choosing the accountants for eCommerce, consider using the below simple checklist to determine if the service provider is right for you.

• Do they understand platforms like Amazon or Shopify?
• Can they handle VAT/IOSS filings?
• Do they use cloud software you can access?
• Are fees clear and fair?
• Will you get regular reports or just year-end accounts?

Consider utilising their free consultation or demo services, and read the testimonials to see if they speak your language (not just accounting jargon)

Why Work with E2E Accounting

E2E Accounting is the leading solutions provider for eCommerce sellers in the UK, offering them an advanced, easy-to-use interface that they can access anytime, anywhere to make decisions. Our clients trust us, as we provide dedicated and custom accounting solutions for Shopify, eBay, Amazon, and more. Your books get reconciled in real-time as they occur, letting you fully utilise the cloud support, and facilitate easier VAT filing and compliance report creation.

Starting from £25/month, we help businesses save time, reduce stress and stay focused on growth. At E2E, we make accounting simple, affordable, and tailored to the platforms you use.

Conclusion

eCommerce accounting is obviously different from traditional accounting. It necessitates an alternative strategy that takes into account the unique opportunities and difficulties of internet business. eCommerce accounting requires precision and experience because it involves managing a large number of transactions, working with numerous currencies, utilising technology for smooth integration, and keeping accurate inventory records. Businesses can establish a solid financial foundation by choosing the right accountants for eCommerce and avoiding typical errors.

Book your free 15-minute consultation today.

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