Running an online store should be about products, customers and reliable fulfilment – not wrestling with spreadsheets and changing tax rules. That’s where specialist e-commerce accountants earn their keep. Selling across Shopify, Amazon, eBay and your own site creates thousands of small transactions, each with fees, refunds and currency quirks. Add VAT rules for cross-border sales, platform reporting changes and the need for clear stock and margin data, and the admin can grow faster than your revenue. We help owner-managed e-commerce businesses put tidy systems in place, keep HMRC happy and get the numbers you need to make better decisions.
Online retail is now a permanent fixture in the UK economy. Internet sales accounted for around 27% of all retail sales in 2024 and have held close to 26–27% through mid-2025 – meaning digital channels are no longer a sideline for many small and medium-sized enterprises (SMEs) (ONS, 2025). As volumes rise, so do the risks of misclaimed VAT, mismatched payouts and unclear profitability by channel. In our experience, the right structure – consistent bookkeeping rules, platform integrations and simple dashboards – turns the finance function from a chore into a growth tool. Below, we break down the key ways dedicated e-commerce accountants support online sellers day to day.
What e-commerce accountants do differently
E-commerce finance has its own patterns. Instead of a few invoices each week, you’re dealing with platform settlements, gateway fees, chargebacks, refunds and gift cards. E-commerce accountants build your chart of accounts to mirror that reality, so data is captured correctly first time. That means splitting gross sales from marketplace and payment fees, recognising VAT accurately, and reconciling returns and discounts. We also set practical rules for stock, landed costs and shipping so your cost of sales is right – and your margins are trusted.
The result is simple: cleaner books, faster close and management reports you can use to make decisions on price, ad spend and inventory.
VAT and international sales without drama
Tax is where online businesses most often need a steady hand. The UK VAT registration threshold is £90,000 of taxable turnover in a rolling 12 months. Once you pass or expect to pass it, you must register – planning early avoids messy backdating and cashflow shocks (HMRC, 2024).
Selling overseas adds more moving parts. For EU consumer orders, schemes such as the Import One Stop Shop (IOSS) and local VAT registrations may be needed depending on your model and fulfilment location. Northern Ireland has its own rules for certain EU-related supplies. We help you choose a compliant route that keeps checkout simple and margins protected, then document it so your team follows the same steps every time.
We also keep you prepared for Making Tax Digital for income tax (MTD IT). From 6 April 2026, unincorporated businesses with qualifying income over £50,000 must keep digital records and send quarterly updates. From 6 April 2027, the threshold drops to £30,000. Setting up the right software and processes now makes the switch painless (HMRC, 2025).
If VAT is a worry right now, our VAT accountants page outlines how we handle registrations, schemes and returns.
Bookkeeping for multiple platforms
Multi-channel sellers need bookkeeping that reflects how money actually moves.
- Sales and fees mapping: Platform statements rarely match bank receipts. We map gross sales, discounts, shipping income, marketplace fees and payment processing charges so every penny is accounted for.
- Refunds and chargebacks: We separate refunds and chargebacks from new sales, ensuring VAT is adjusted correctly and customer service trends are visible.
- Foreign currency: For USD/EUR sales, we post at the right exchange rates and handle foreign exchange differences cleanly.
- Stock and landed costs: We capture inbound freight, duty and packaging against inventory, so gross margins are real, not optimistic.
We pair these rules with tidy monthly schedules so reconciliations happen on time and the month end is calm.
Cashflow management that fits retail cycles
Even profitable stores can run short of cash during restocks or peak ad campaigns. We build simple cashflow forecasts that reflect reality – lead times, third-party logistics pay cycles, platform payouts and VAT due dates. That helps you spot pinch points early and prioritise spend. Typical quick wins include the following.
- Payment terms: Negotiate with suppliers to align stock purchases with sales peaks.
- VAT schemes: Cash accounting or annual accounting can help some sellers smooth payments.
- Ad spend pacing: Tie budget to contribution margin by channel to avoid overspend during slower weeks.
With better visibility, you can plan inventory confidently without tying up funds unnecessarily.
Integrating accounting software with sales channels
Clean data comes from good integrations. We typically use Xero as your accounting hub and connect marketplaces and carts via reliable connectors such as A2X. This lets you do the following.
- Automate postings: Settlements post to the right nominal codes with VAT split correctly, saving hours each week.
- Match bank receipts: Payouts from Amazon, Shopify Payments, PayPal and Stripe reconcile against automated journals.
- See channel performance: Standardised data makes it easy to compare margins across channels and products.
If you’re starting from scratch, we’ll design the chart of accounts and tracking categories, then test each connector with sample data before going live. If you already have a set-up, we’ll review, tidy and document it so your team can run it with confidence. Read more about our approach on our e-commerce accounting page.
Practical growth advice from accountants who know e-commerce
Once the basics are sorted, the right advice moves the needle. We focus on actions that improve contribution and cash.
- Pricing and fees: Use marketplace fees analysis to identify the real cost of each channel to set sustainable pricing.
- Product mix: Analyse the stock-keeping unit performance to highlight high-volume, low-margin products and where a small price change lifts profit.
- Operations: Look at fulfilment costs to compare courier and third-party logistics options with clear per-order costings.
- Working capital: Prepare lender-friendly forecasts for stocking up ahead of peak seasons.
- Key performance indicators: Track average order value, repeat rate, return rate and gross margin by channel – not just top-line sales.
Because the accounts are structured for e-commerce, these reviews are quick to run and easy to repeat each month.
How we keep you compliant and in control
Compliance should be routine, not stressful. We make sure the core obligations are handled on time and with minimal fuss.
- VAT returns and on-time submissions: Quarterly filings with records that stand up to review (and tidy audit trails).
- Digital records: MTD-ready systems mean clean, connected software with clear workflows and permissions.
- Fast close for year end: Pre-year-end checks to smooth stock valuation, accruals and director sign-off.
Ready to feel on top of your numbers?
If you sell online, you don’t need a bigger spreadsheet – you need a set-up designed for e-commerce. E-commerce accountants build orderly books, keep VAT right and deliver the data that helps you decide what to stock, where to sell and when to invest. With integrations handling the detail and clear reporting each month, you can focus on customers while staying compliant and cash-positive. The shift to digital record-keeping is also gathering pace, with MTD IT arriving for larger sole traders and landlords from 6 April 2026 and more from 6 April 2027 – sorting your systems now will save headaches later (HMRC, 2025).
If you’d like a practical review of your set-up, we can help with a quick diagnostic across platforms, VAT, bookkeeping and cashflow, then implement the fixes. Start with our e-commerce accounting service, explore how we manage VAT for sellers on our VAT accountants page or get in touch to book a call. Talk to our e-commerce accountants about getting clean data, simpler compliance and steadier cashflow – and turn your numbers into a genuine advantage.
