E-Commerce Accountants UK for Shopify, Amazon & Online Sellers

Not necessarily. A suitably experienced accountant may be able to support an e-commerce business, but relevant e-commerce experience can be valuable where there are multiple marketplaces, payment processors, inventory systems, international sales or complex VAT requirements. The important point is that the accountant understands how the seller’s platforms and transaction flows affect the accounting records.

We support a range of major e-commerce platforms, including Shopify, Amazon FBA, eBay, Etsy, WooCommerce and TikTok Shop, as well as payment processors such as PayPal, Stripe and Klarna. Depending on your setup, integration tools such as A2X or Link My Books can help transfer sales, fees and refunds into accounting software such as Xero or QuickBooks and reduce manual data entry. The exact setup will depend on your selling platforms, payment flows and accounting requirements.

Our cloud accounting services can help with software setup, migration and ongoing accounting support.

A UK-established business normally needs to register for VAT if its taxable turnover for the previous 12 months goes over £90,000, or if it expects its taxable turnover to go over £90,000 in the next 30 days. Businesses can also register voluntarily below the threshold. Different rules can apply to businesses established outside the UK, including situations where VAT registration may be required regardless of turnover.

See our VAT Registration UK guide for the detailed rules and deadlines.

Making Tax Digital for VAT applies to VAT-registered businesses, which must keep the required digital records and use compatible software for VAT reporting. Making Tax Digital for Income Tax now applies from 6 April 2026 to qualifying sole traders and landlords whose qualifying income was over £50,000 in 2024/25. It extends to qualifying income over £30,000 from 6 April 2027 and over £20,000 from 6 April 2028. These Income Tax rules apply to qualifying individuals rather than limited companies.

Our fees are transparent, fixed monthly packages — no hourly rates and no surprise invoices. The exact cost depends on your sales volume, number of platforms, and the level of support you need. Packages typically start from a monthly retainer covering bookkeeping, VAT returns, and a dedicated accountant. We provide a clear, itemised quote before you commit to anything. Call us on 0333 023 1300 or book a free consultation to get a proposal tailored to your business.

We primarily use Xero and QuickBooks Online, both of which are MTD-compliant and integrate seamlessly with major e-commerce platforms and payment processors. Depending on your setup, we also use specialist integration tools such as A2X (for Amazon and Shopify) and Link My Books (for multi-platform sellers) to automate the flow of sales data, fees, and refunds into your accounting software. You don’t need any accounting knowledge to use these systems — we handle everything and give you clear monthly reports.

Absolutely. Many of our clients come to us before they’ve made their first sale — and we think that’s the smartest time to start. Setting up the right business structure, choosing the correct accounting software, understanding your VAT obligations from day one, and building clean financial records from the outset saves enormous time, cost, and stress later. Whether you’re launching on Shopify, listing your first products on Etsy, or preparing an Amazon FBA launch, we’ll help you build the right financial foundation.

Yes. We can support Amazon FBA sellers with settlement reconciliation, bookkeeping and the VAT and accounting requirements relevant to their circumstances. Cross-border VAT obligations can depend on where stock is held, where goods move and the fulfilment arrangements being used, so the correct treatment needs to be considered for each seller’s setup.