Shopify accountant UK
Accounting for Shopify stores that actually matches your sales, refunds, payment fees and payouts.
In short: NDCA is an ACCA-regulated accountancy practice for UK Shopify store owners. We reconcile Shopify Payments, PayPal and app fees, handle VAT and stock and prepare your Self Assessment or limited company accounts. Your agreed services are covered by one fixed monthly fee, with a named accountant who knows your numbers.
NDCA works with store owners from your first sale through to a multi-channel brand running paid acquisition across several markets. We handle bookkeeping, VAT, Corporation Tax and Self Assessment, with a named accountant who understands how Shopify settles your money.
What NDCA clients say
Verified Google reviews from NDCA clients.
In short: NDCA is an ACCA-regulated accountancy practice for UK Shopify store owners. We reconcile Shopify Payments, PayPal and app fees, handle VAT and stock and prepare your Self Assessment or limited company accounts. Your agreed services are covered by one fixed monthly fee, with a named accountant who knows your numbers.
NDCA works with store owners from your first sale through to a multi-channel brand running paid acquisition across several markets. We handle bookkeeping, VAT, Corporation Tax and Self Assessment, with a named accountant who understands how Shopify settles your money.
How Shopify store owners get paid
Shopify income rarely shows up as one clean number, and the mix of platform, app and processor fees is different for every store.
Sales, refunds, fees and payouts
We know Shopify stores move money through several systems at once: orders, refunds, discounts, fees, Shopify Payments, Stripe, PayPal and chargebacks. We reconcile all of it so your revenue and margin figures stay accurate.
Shopify Payments, Stripe and PayPal
Shopify Payments settles in payouts with fees, refunds and adjustments already netted off, so your bank statement shows a net figure rather than gross sales. If you also use Stripe, PayPal or another gateway, each settles separately with its own balance and schedule. We bring every gateway into Xero and reconcile each payout against your order data.
Multi-channel sellers
Shopify can be your main store without being your only sales channel. If you also sell on Amazon, eBay, Etsy or TikTok Shop or run wholesale, we bring every channel into one set of accounts. See our Amazon FBA accountant page, or our wider e-commerce accountant hub if you trade across several platforms.
Tax and VAT for Shopify store owners
Shopify makes it easy to sell to customers anywhere, which is exactly what makes the VAT position complicated.
VAT for Shopify stores
UK VAT registration is generally required once your taxable turnover exceeds £90,000. Your VAT position also depends on what you sell, where your customers are located and how your sales are structured, not simply what Shopify reports.
Overseas sales
Selling to customers outside the UK can introduce extra VAT and tax considerations, depending on your customer’s location, whether they are a business or consumer and where your goods are shipped from.
Stock and cost of goods sold
Turnover alone does not show profitability, £100k of sales does not mean £100k of profit. We track cost of goods sold, including supplier costs, freight and import duty, whatever your stock model.
Sole trader or limited company
There is no fixed income level at which becoming a limited company automatically makes sense. The right structure depends on your profits, personal income needs, other income, how much you plan to leave in the business and your longer-term plans. NDCA can compare the options using your actual figures.
We also handle your bookkeeping, VAT returns, annual accounts and Corporation Tax.
How NDCA works
What you can expect:
We work with e-commerce sellers specifically, so we already understand Shopify Payments, payment gateway payouts and app subscription costs. You pay one fixed monthly fee, your numbers stay current in Xero, and you get a named accountant who normally replies the same day.
The software we use: Xero and Link My Books
Modern tools built for how Shopify actually pays store owners.
We run your bookkeeping through Xero, connected to Link My Books, which breaks each Shopify and payment gateway payout down into sales, refunds, fees and VAT rather than one unexplained lump sum. We also use Apron to capture your receipts and supplier bills and send them into Xero.
Shopify accountants across the UK
NDCA works remotely with clients across the country, wherever your business is based.
Shopify payouts and app fees a mess?
Payments, refunds, apps and VAT all reconciled properly, every payout.
Reviews
Discover why businesses trust us for dependable accounting services and practical financial advice.
What NDCA clients say
We work with businesses across the UK and beyond, delivering results that speak for themselves. Browse our reviews to see the impact we have made, and if you have worked with us, we would love for you to leave a review on Google
Switching accountants is easier than you think
NDCA handles the switch for you. We contact your existing accountant, request professional clearance, arrange the transfer of your records and handle the necessary paperwork. How long it takes depends mainly on how quickly your previous accountant sends the records across, and we keep you updated throughout.
Shopify store tax at a glance (2026/27)
View the key tax figures
| Income covered | Shopify orders, less payment and app fees, refunds and chargebacks |
|---|---|
| Trading allowance | If your total trading sales are £1,000 or less in a tax year, you do not need to declare them. Above that, you can deduct £1,000 instead of your actual costs and must register for Self Assessment by 5 October after the tax year ends |
| Platform reporting to HMRC | Sales through your own Shopify store are not reported, because Shopify provides the shop and does not sell for you. Sales on marketplaces such as Amazon, Etsy or eBay are reported to HMRC each January, unless you make fewer than 30 sales worth €2,000 (about £1,700) or less in a calendar year |
| VAT registration | Compulsory above the £90,000 threshold |
| VAT on your own store | On your own Shopify store you charge and account for the VAT yourself. The rule that makes a marketplace collect the VAT only applies to marketplace sales, for overseas sellers and imports of £135 or less |
Figures are for the 2026/27 tax year and were checked against GOV.UK guidance. Income Tax and Corporation Tax rates are on our e-commerce accountant page.
Shopify store accounting FAQs
Our fees start from £95 plus VAT a month for limited companies, with no setup fee. Self Assessment starts from £245 plus VAT as a one-off fee. You receive a fixed quote at the end of your free 30-minute call, based on your turnover, transactions, VAT, payroll and number of directors. Any records alignment or bookkeeping catch-up is quoted separately in writing before work starts.
Yes, once your UK taxable turnover passes £90,000 in any rolling 12 months or you expect turnover in the next 30 days alone to go over £90,000. Sales to overseas customers and digital products follow different VAT rules, so we check how your sales are structured.
It depends on your profits, how much you take out and your plans for the business, so there is no single figure. We compare both structures using your real numbers before you decide.
Related guides
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Ready to get your accounts under control?
Get Shopify payouts, app fees and multi-channel sales sorted with fixed monthly fees.
