Bookkeeping & Accounting for E-Commerce Businesses UK
E-commerce accounting is more complex than most business owners realise. Between multiple sales channels, marketplace fees, cross-border VAT, inventory management, and payment gateway reconciliations, the bookkeeping challenges facing online sellers are significant. At ProKeeper, we specialise in accounting and bookkeeping for e-commerce businesses across the UK — helping you stay compliant, understand your true profitability, and grow with confidence.
The Unique Accounting Challenges for E-Commerce
Running an online store comes with financial complexity that general accountants often aren’t equipped to handle well. Common challenges include reconciling high transaction volumes from platforms like Shopify, Amazon, eBay, Etsy, and WooCommerce; managing marketplace fees and refunds; handling VAT on UK and international sales; calculating COGS (cost of goods sold) and gross margin by product; managing stock and inventory valuation; and dealing with PayPal, Stripe, and other payment gateway settlements that don’t match your bank deposits directly.
Our E-Commerce Accounting Services
- E-commerce bookkeeping — automated reconciliation of your Shopify, Amazon, eBay, or WooCommerce transactions with your bank and payment gateways
- VAT for online sellers — UK VAT, OSS (One Stop Shop) returns for EU sales, and guidance on international VAT obligations
- Amazon and marketplace accounting — understanding and reconciling the complex settlement reports from Amazon Seller Central and similar platforms
- Inventory and COGS management — we set up your accounting system to accurately track stock values and calculate cost of goods sold
- Profitability reporting — monthly reports showing your true profit margin after all platform fees, shipping, returns, and advertising costs
- Corporation tax and self assessment — accurate annual accounts and tax returns, whether you operate as a sole trader or limited company
VAT for E-Commerce Sellers in the UK
If you sell goods to consumers in the UK and your turnover exceeds £90,000, you must register for UK VAT. If you also sell to EU consumers, you may need to register for the EU’s One Stop Shop (OSS) scheme or register individually in EU countries depending on your sales volumes and routes to market. For businesses importing goods, import VAT and customs duty need to be correctly accounted for. Our e-commerce VAT specialists ensure you’re fully compliant without overpaying. See our dedicated VAT Returns service.
Cloud Accounting for E-Commerce
We use Xero integrated with tools like A2X, Dext, and Link My Books to automate the reconciliation of your e-commerce data. This means accurate books with minimal manual effort — and real-time visibility into your numbers. We’ll set up your accounting stack, connect your platforms, and keep everything running smoothly.
E-Commerce Accounting Pricing
Pricing for e-commerce bookkeeping and accounting depends on your transaction volumes, number of sales channels, and the complexity of your VAT position. Packages start from £200 per month. Contact us for a tailored quote.
Frequently Asked Questions — E-Commerce Accounting
Do I need to charge VAT on international sales?
It depends on where your customers are and the nature of the goods. Sales to UK consumers require UK VAT above the threshold. Sales to EU consumers may require OSS registration. Sales to consumers outside the UK and EU are generally zero-rated. Our VAT team will map your sales flows and advise on exactly what’s required.
How do you handle Amazon’s complex settlement reports?
Amazon’s settlement reports combine sales, refunds, fees, and reimbursements in a way that doesn’t directly match your bank deposits. We use specialist tools to automatically parse and reconcile Amazon settlement data with your accounting records, giving you accurate revenue and fee figures.
Get Specialist E-Commerce Accounting Support
Don’t let complex accounting hold back your online business growth. ProKeeper’s e-commerce accounting specialists will get your books in order and keep them that way.