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E-commerce and marketplace sellers

E-commerce accountants for Shopify and Amazon sellers

For UK sellers on Shopify, Amazon, eBay and Etsy. Marketplace payments often arrive in your bank account as one net figure after fees, refunds and VAT adjustments. We break that payment back down into the full transaction detail, so your accounts show your real sales, costs and margins, not just the amount the platform paid out.

UK independent product stockroom with shelves of colourful packaged goods, industrial windows and warm natural light.
01
Is this for me?
We work with sellers on Amazon, Shopify, eBay, Etsy and direct-to-consumer: businesses dealing with marketplace net payouts, the Online Marketplace VAT rules where the platform becomes the deemed supplier, and multi-platform reconciliation across channels that each bill differently.
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What's covered
Marketplace reconciliation from settlement reports, Online Marketplace VAT and cross-border VAT registration, inventory and cost-of-goods accounting, regular management accounts, and the tax planning behind multi-platform trading.
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What it costs
Pricing tracks platform mix and monthly settlement volume more than headline turnover. The fees page sets out the bands.

Net payouts explained

Marketplaces like Amazon and Shopify deposit a single "Net Payout" into your bank account. That deposit has already had seller fees, shipping costs, and customer refunds deducted. The platform's settlement report is the only place those components are itemised.

Recording the deposit as "Sales" understates your gross turnover, miscalculates your VAT position, and hides what the platform charged you to sell. Getting this right means breaking every deposit back into its component parts.

Marketplace reconciliation

How marketplace payouts are reconciled

We set up software integrations like Link My Books and A2X to break those deposits down from the settlement reports.

The settlement data is categorised in your digital bookkeeping software. Gross sales are recorded against the right product lines, payment-gateway fees (Stripe, PayPal, Klarna) are mapped to expenses, and the VAT position is calculated against current HMRC treatment rather than reconstructed at quarter-end. Our UK VAT guide covers Standard VAT, the Flat Rate Scheme, Cash Accounting, and the 16.5% limited-cost-trader rate that can make the Flat Rate Scheme expensive once cross-border volumes change the cost mix on your return.

E-commerce sellers

We track cost of goods per product, handle VAT across the countries you sell into, and reconcile your payouts against each marketplace settlement.

VAT, OSS & IOSS

Cross-border selling creates a multi-jurisdiction VAT position that has to be set up correctly from the start. UK VAT, the EU One-Stop Shop (OSS) and Import OSS each have their own registration triggers, return cycles and treatment of marketplace deemed-supplier rules. We break down your sales by destination, register you on the right schemes, and submit each VAT return from reconciled platform data rather than reassembled spreadsheets.

Landed costs (COGS)

Your margin is not just sale price minus manufacturing cost. We track freight, customs duties, and 3PL storage so each SKU has a Cost of Goods Sold (COGS) figure you can rely on.

Stock, adverts and margin

Through our management accounts, we review Return on Ad Spend, customer acquisition cost, and inventory turnover so you can judge whether to commit more cash to stock.

MTD digital links

HMRC's MTD (Making Tax Digital) rules forbid manual copy-pasting of financial data between systems. We build the digital links from your sales platforms into MTD-compatible cloud accounting software, so the audit trail matches HMRC's expectations.

Company structure

When turnover grows, a limited company structure can reduce personal tax and separate business liabilities. We manage the transition to a Limited Company and the ongoing accounts that follow.

Corporation Tax

We calculate your year-end Corporation Tax ahead of time, including director remuneration, dividend decisions and the return itself, so the liability is known well before it lands.

Frequently asked questions

How do you reconcile Shopify and Amazon payouts?

Marketplaces deposit net payouts, which already have fees, refunds and shipping deducted. We use integration software like A2X or Link My Books to break those deposits down, so gross sales, individual fees, refunds and VAT each land against the right ledger line instead of collapsed into a single revenue figure.

Do I need to charge VAT on my e-commerce sales?

If your rolling 12-month taxable turnover exceeds the UK VAT threshold, you must register. When you sell internationally, the rules change. We help you navigate domestic VAT, zero-rated international exports, and the EU One-Stop Shop (OSS) thresholds.

What are 'Landed Costs' and why do they matter?

Landed cost is the total price of getting your product to the customer, including manufacturing, sea or air freight, customs duties, and 3PL storage. We include this in your management accounts so you can see the margin per item and price with the full cost in front of you.

Want to know what your store is making?

A short call with an accountant who works with online sellers. We look at the payout data, the landed-cost picture per SKU, and the digital links into your accounting software, then come back with a written proposal.

Request a consultation