- Ecommerce accountant fees run from about £150 to £3,700+ a month plus VAT
- Each extra channel, store and payment gateway adds reconciliation work
- Crossing the £90,000 VAT threshold adds quarterly VAT returns to your bill
Ecommerce accountant cost in the UK runs from about £150 a month plus VAT for a small marketplace seller to more than £3,700 a month for a multi-channel brand selling abroad. An ecommerce accountant prices on your sales channels, order volumes and VAT position, so those three drive most of the bill. This guide covers costs by stage, the extras and what to check in a quote.
How much does an accountant for an ecommerce business cost?
Most online sellers pay somewhere between £150 and £650 a month plus VAT. Fees climb past £2,000 a month once you’re running several stores, selling into other countries or asking for monthly management accounts.
The table uses worked examples from Elver E-Commerce Accountants’ published pricing (April 2026), one of the few UK ecommerce specialists to show full packages. Each fee includes software, so treat it as your total monthly cost rather than a pure accounting fee.
| Business stage | What’s covered | Monthly fee (+ VAT) |
|---|---|---|
| Start-up: Amazon UK only, £75,000 turnover, you do the bookkeeping | Year-end accounts, corporation tax return, confirmation statement, director payroll, software | £150 |
| Growing: one Shopify store, £1m turnover, three payment gateways | The above plus bookkeeping, quarterly VAT returns, payroll for five and two Self Assessment returns | £642 |
| Established: Amazon UK, EU and US, two Shopify brands, Etsy, £5m turnover | The above plus monthly management accounts and forecasts | £2,096 |
| International: four channels, £10m turnover, VAT and GST abroad | The above plus overseas VAT and GST filings | £3,704, plus £28,000 a year |
For comparison, a general online guide from myPOS puts limited company accountant fees at £100 to £250 a month, rising to £150 to £400+ once you’re VAT registered. Ecommerce sits at the top of that range because of the extra reconciliation work.
If you want the general picture first, our guide to limited company accountant cost covers it. Accountant fees are also just one line in the wider cost of running a limited company.
What affects ecommerce accountant fees?
Ecommerce accountant fees follow the work, not your turnover. Reconciling a small payout takes almost as long as a large one, so volume and complexity matter more than revenue.
A consultant with one client and no stock needs far less work, which is why contractor accounting costs sit lower. These are the factors that move an ecommerce quote.
How many channels and stores you run
Every marketplace and store produces its own sales, fees and payout reports. An accountant has to match each one to your bank, so a second Shopify store or a move onto Etsy adds a separate monthly line.
This is why a shopify accountant cost quote is usually priced per store. Amazon seller accountant cost tends to be priced per region instead.
Your order volumes and payment gateways
More orders mean more transactions to check. Extra gateways like PayPal and Klarna add timing differences between what your store reports and what lands in the bank. They’re a big reason one shopify accountant cost quote can be several times another.
Whether you’re VAT registered
You must register once your taxable turnover passes the £90,000 VAT threshold in any rolling 12 months. From then on, your accountant files quarterly VAT returns, which usually means a higher monthly fee or a per-return charge.
Who does the bookkeeping
Doing it yourself keeps the ecommerce bookkeeping cost down. In the start-up example above, the seller handles their own books and pays about a quarter of the growing business’s fee.
Staff and directors
Payroll is priced per employee, and each director’s Self Assessment return is usually charged separately. Both are easy to miss when you compare headline fees.
What ecommerce-specific work costs extra?
A general accountant prices a limited company on filings. An online seller accountant in the UK also prices the work that only exists because you sell through platforms.
Marketplace payout reconciliation
Amazon, eBay and Etsy pay you a net figure after taking referral, fulfilment and advertising fees. Your accounts need the gross sales and each fee recorded separately, or your margins and VAT figures will be wrong.
That work drives most of the amazon seller accountant cost. Elver lists Amazon revenue reconciliation at £32 a month plus VAT per region, against £31 to £1,140 a month per Shopify store.
Multi-channel sales
Selling on three platforms means three sets of reports, refunds and fees to line up. A good online seller accountant in the UK shows you profit by channel, so you know where to spend your next marketing pound.
VAT on overseas sales
Goods you send outside the UK can be zero-rated, but only if you keep valid proof of export. Selling into the EU or US can also bring local VAT or sales tax registrations, and those filings are priced on top.
In Elver’s £10m example, overseas VAT and GST filings add £28,000 a year plus a monthly charge. That’s the single biggest jump in the table.
Stock
If you hold stock, including stock in Amazon’s warehouses, it has to be counted and valued at year end. HMRC accepts the lower of cost and net realisable value, so slow-moving or damaged stock needs writing down.
What should you check in an ecommerce accountant’s quote?
Ecommerce accountant fees are only comparable if the scope is. One of the most common questions in Sleek’s UK sales calls is whether a quoted fee includes setup, so ask about the extras up front.
Check that each quote states:
- Which channels and stores are priced in. Adding a new marketplace mid-year shouldn’t come as a surprise invoice.
- Order or transaction caps. Find out what happens to the fee if a strong quarter takes you over the limit.
- How VAT returns are charged. Some firms include them, others bill per return.
- Any catch-up or onboarding fee. Joining partway through your financial year often adds a one-off charge.
- Who your named accountant is. Ask how quickly they reply, especially in the weeks before a VAT deadline.
- What counts as extra advice. A quick question about a new channel shouldn’t be billed as a project.
When is a generalist accountant the better call?
A specialist isn’t always worth the extra. If you sell on one UK marketplace, sit well under the VAT threshold and use a connector app to pull in your sales, a good limited company accountant can usually handle it.
At the other end, a £10m brand with US sales tax and several EU VAT registrations may need a firm with its own international VAT team. Pick the accountant that matches where your business is going, not just where it is today.
How Sleek helps with ecommerce accounting
Sleek gives your limited company a named, qualified accountant who replies the same day. AI does the routine bookkeeping, your accountant checks it, and you can see what was done and what was approved.
That leaves you with clean numbers by channel, so you can decide where to grow next. Our accounting services cover your bookkeeping, year-end accounts, corporation tax and VAT returns in one relationship.
Plans run from Starter at £900 a year plus VAT to Enterprise at £399 a month plus VAT. Pro, at £200 a month plus VAT, adds monthly bookkeeping and quarterly VAT returns.
Know your ecommerce accountant cost before you commit
Prices may vary with current promotions, check the latest on the relevant page.
FAQs on ecommerce accountant cost
Do I need a specialist ecommerce accountant?
You need one once you sell on more than one channel, hold stock or sell abroad. Below that, a general limited company accountant who understands marketplace payouts can do the job. The test is whether they can show you profit by channel, not just file your accounts.
Is a monthly fee better than a one-off year-end fee?
A monthly fee spreads the cost and usually includes regular bookkeeping and support, so problems get caught early. A one-off year-end fee can look lower but often leaves months of marketplace data to untangle at once. For a VAT-registered seller filing quarterly, a monthly fee is usually the better fit.
What should be included in an ecommerce accountant's fee as standard?
Every quote should cover the statutory filings for a limited company: annual accounts for Companies House, the Company Tax Return and the confirmation statement. VAT returns should be included once you’re registered. Anything else, such as payroll or management accounts, should be itemised.
Are accounting software and connector apps included in the fee?
Sometimes. Some ecommerce firms bundle Xero and a connector such as A2X into the monthly fee at a partner discount, while others expect you to pay for them separately. Ask for the software cost as its own line so you can compare quotes fairly.
Can I do my own bookkeeping to lower the cost?
Yes, and it’s the simplest way to cut your ecommerce bookkeeping cost early on. You’ll still need clean records your accountant can rely on, so it works best with a connector app that pulls in each marketplace’s sales and fees. Once order volumes grow, handing it over usually saves more time than it costs.
Do marketplace fees reduce my turnover for the VAT threshold?
No. Your VAT taxable turnover is based on what your customers paid, not the net payout after Amazon or eBay take their fees. A seller with £85,000 of payouts could already be over the £90,000 threshold once fees are added back.
Will HMRC know about my marketplace sales?
Yes. Under the reporting rules for digital platforms, marketplaces report seller details to HMRC each year, unless a seller makes fewer than 30 sales and receives under about £1,700. Your accounts should match what the platforms report.
