Amazon seller accountant
eCounts is an Amazon seller accountant for UK businesses selling through Seller Central. We reconcile every settlement, split out every fee, value your stock wherever it sits and get your Amazon VAT position right, so the margin in your accounts is the margin you actually make.
Led by an ICAEW chartered accountantSettlements reconciled into Xero or QuickBooks via A2XFixed monthly fee, rolling agreementIn short
eCounts provides specialist accounting for Amazon sellers in the UK, covering FBA and FBM. We turn Amazon settlements into accurate accounts, separating sales, fees, refunds, advertising and stock, and we handle Amazon-specific VAT, including marketplace collection rules and EU sales. It suits sellers who have outgrown a generalist accountant or a bank-feed bookkeeping setup.
Platforms we reconcile every month
Trademarks belong to their owners. eCounts is independent and not endorsed by these platforms.
What usually goes wrong
The most common problem we see is the Amazon deposit posted to the books as a single sales figure. Revenue is understated, every fee disappears into the net amount, and the gross margin in the accounts is a guess.
From there it compounds. Refunds are netted off invisibly, advertising sits in one cost line, stock at Amazon is never counted, and VAT is calculated on the deposit rather than the sales.
An Amazon seller accountant fixes this at the source: the settlement report, not the bank line. That is what our multi-platform reconciliation is built around, with landed cost accounting feeding the true cost of every unit you import.
How Amazon money works
Amazon does not pay you for each sale. It collects everything into a settlement period, usually around 14 days, then pays out one net amount. That deposit is your sales, less referral and fulfilment fees, less refunds, less advertising, less storage and other charges, plus or minus any reimbursements.
Amazon can also hold back a reserve against future refunds, which rolls into the next settlement, and can defer payment on orders until they are delivered.
Settlements rarely align with calendar months, so each one needs splitting across the right months. Correct Amazon accounts show sales, each fee type, refunds and reserves separately, with the net matching the bank. That is the standard our bookkeeping and management accounts work to, and it is what makes cash flow forecasting possible.
Amazon fees
Which fees apply depends on your marketplace, your category and whether you use FBA. These are the main lines we post separately so you can see your real fee load.
| Fee | What it is | Why it matters to margin |
|---|---|---|
| Referral fee | A percentage of each sale, set by category | Usually the biggest single fee, and it varies by product |
| FBA fulfilment fee | Per-unit pick, pack and delivery charge | Driven by size and weight, so packaging changes can move it |
| Storage fees | Monthly charge for space in Amazon's warehouses, higher in Q4 | Slow-moving stock quietly eats margin |
| Aged inventory surcharge | Extra charge on stock held too long | Often the fee sellers did not know they were paying |
| Returns and refund fees | Returns processing and the refund administration fee | A refunded sale can still cost you money |
| Removal and disposal | Charges to send back or destroy stock | Needs matching to stock write-downs at year end |
| Advertising | Sponsored Products and other Amazon Ads spend | Belongs in contribution margin, not general overheads |
Amazon Xero integration
A bank feed only sees the net deposit. A2X reads the settlement itself.
Each settlement report lists every order, fee, refund, reimbursement and reserve movement for the period.
A2X groups those lines into a summarised journal, mapped to the right accounts and VAT codes, split by month where a settlement crosses a month end.
One entry per settlement lands in Xero or QuickBooks, not thousands of order lines.
The journal's net figure matches the Amazon deposit exactly, so reconciliation is a single match.
Free calculator
Put in your selling price, landed cost and fees to see what one unit actually earns after VAT, Amazon's fees and advertising, and the price you would need for a 30% margin.
Per sale
Profit per sale
£0.00
0% margin on net sales
Price needed for a 30% margin: £0.00
An estimate for planning, not tax advice. Default fees are examples checked in October 2026; platforms change rates, so use the figures on your own fee invoices. Excludes storage, returns processing and the £25 a month Professional plan.
Get your real margins checked
FBA accounting
Many sellers run both. The difference is where stock sits and where fulfilment cost lands.
Fulfilled by Amazon (FBA)
Stock sits in Amazon's network, still owned by youFulfilment and storage come off the settlement as feesInbound shipping to Amazon is part of landed costAged and unsellable stock needs regular reviewFulfilled by merchant (FBM)
Stock sits with you or a 3PLCarriage and packaging are your own supplier costs3PL invoices need matching to ordersMargin looks higher until delivery costs are includedBeyond the settlement
Stock may be at Amazon, at a 3PL, on the water or at home. We value it at year end and build cost of goods sold from landed cost, including freight and duty.
Category-level COGS on BasicSKU-level COGS on GrowthWrite-downs for aged and unsellable stock
Selling on amazon.com or EU marketplaces means sales in dollars or euros. How they convert, and how exchange differences are recognised, changes your margin.
Multi-currency on Scale
Ad spend tells you more when it sits against the products it sold. We show it as part of contribution margin, alongside measures such as ACoS and TACoS.
Paid ads reconciliation on Scale
Settlement cycles plus long stock lead times squeeze growing Amazon businesses. We forecast cash so stock orders and any Amazon lending are planned.
Cash flow forecasting on GrowthTax for Amazon sellers
How UK Amazon sellers pay tax depends on business structure. As a sole trader, your Amazon profit is taxed through Self Assessment: Income Tax above the £12,570 Personal Allowance, plus Class 4 National Insurance at 6% on profits between £12,570 and £50,270 for 2026/27. As a limited company, the business pays Corporation Tax on its taxable profit, at 19% up to £50,000 and 25% above £250,000, with marginal relief in between.
Either way, taxable profit starts from gross sales in Amazon Seller Central, not the deposits in your bank. Fees, advertising, refunds and cost of goods are deducted from there, and inventory valuation at the year end decides how much of your stock purchases count as a cost this year. Getting stock wrong moves profit, and tax, between years.
An Amazon FBA accountant brings all of this together: accounting software fed by settlement data, financial reports you can act on each month, and the tax compliance and VAT compliance that sit on top. For sellers whose profits are growing, we also review each year whether a limited company would be more tax-efficient.
Amazon seller VAT
If your business is established in the UK and sells goods already in the UK to UK customers, you account for the VAT on your own return once registered. Amazon does not do it for you. You must register when taxable turnover in any rolling 12 months goes over £90,000, or when you expect it to in the next 30 days.
Amazon accounts for the VAT instead when the seller is not established in the UK and the goods are in the UK, and on consignments of £135 or less sold from outside the UK to customers in Great Britain. For overseas sellers the £90,000 threshold generally does not apply.
Amazon checks where sellers are established, looking at where decisions are made, where directors live, bank details and addresses. A UK company with only a virtual office may not pass, and if Amazon treats you as non-established it collects VAT on your UK sales.
Goods sent from Great Britain to EU customers leave the UK as exports and are imported into the EU. Storing stock in EU warehouses, for example through Pan-European FBA, usually means registering for VAT where the stock is held. Our VAT returns and MTD service covers all of this, and importers can use postponed VAT accounting to avoid paying import VAT upfront.
Top tips
Each settlement report lists every order, fee, refund, reimbursement and reserve behind a payout. Download them from Seller Central and keep them, because they are the source for accurate accounts and VAT returns.
Referral fees scale with price but FBA fees are fixed per unit, so a rise in freight or duty hits cheaper products hardest. Check a product with the import duty calculator before you reorder.
Amazon charges higher monthly storage fees from October to December. Sending in only what will sell through the peak protects margin and cash.
If advertising costs more per sale than the unit earns before ads, every extra sale loses money. The calculator above shows that break-even point.
Amazon issues VAT invoices for its seller fees in the Tax Document Library. A VAT-registered seller needs them to support the VAT reclaimed on fees.
From the accountant
“Most Amazon sellers know their sales to the penny and their margin per ASIN not at all. Once landed cost and FBA fees sit side by side, the loss-making products are usually obvious within the first month.”
Key facts for 2026
8–15% is the range of most Amazon UK referral fees, with 15% for categories not listed separately, plus £25 a month (excl. VAT) for the Professional plan.
October 2026. Source: Amazon, Selling on Amazon fees (sell.amazon.co.uk)
£90,000 is the UK VAT registration threshold, tested on taxable turnover over any rolling 12 months.
2026/27, unchanged since 1 April 2024. Source: GOV.UK, Register for VAT
30 sales or about £1,700 (€2,000) in a calendar year is the point at which online platforms must report a seller's details and income to HMRC.
2026, rules in force since January 2025. Source: GOV.UK, Reporting rules for digital platforms
25% is the main rate of Corporation Tax for profits over £250,000, with a 19% small profits rate up to £50,000 and marginal relief between.
2026/27, rates unchanged since 1 April 2023. Source: GOV.UK, Corporation Tax rates and allowances
Figures checked 9 October 2026. Rates and thresholds change, so check the source before relying on them.
Coming up
Import costs, VAT invoicing and Income Tax rules are all changing over the next few years. Each date links to the official source.
Sole traders and landlords with qualifying income over £30,000 in 2025/26 must keep digital records and send quarterly updates. Online sellers should check their gross sales, not profit, against the threshold.
Source: GOV.UK, Find out if and when you need to use MTD for Income Tax
From the 2027/28 tax year, each late quarterly update earns a penalty point, and four points means a £200 penalty. 2026/27 is the year to get the routine right.
The threshold drops again, based on 2026/27 income, bringing many smaller Etsy, eBay and side-business sellers into quarterly digital reporting.
Source: GOV.UK, Find out if and when you need to use MTD for Income Tax
Since 1 July 2026 the EU has charged a flat €3 customs duty per item on parcels worth up to €150. From July 2028 normal duty rates apply, so UK sellers shipping to EU consumers should expect landed costs to change again.
Source: European Commission, Temporary flat fee on low-value imports
The government will require all VAT invoices to be issued and received electronically from 2029, with a roadmap due at Budget 2026. Accounting software choices made now should support it.
Source: GOV.UK, Promoting electronic invoicing: consultation response
Announced at Autumn Budget 2025: imports of £135 or less will no longer be duty-free, with new customs arrangements for these goods. Sellers who import small parcels should review their landed costs.
Source: GOV.UK, Reforming the customs treatment of low value imports
Book a discovery call and we will look at how your settlements, fees, stock and VAT are handled today, and what would change.
Example dashboards
Profit per ASIN after landed cost and FBA fees, Amazon alongside your other channels, and a cash forecast that knows when stock has to be paid for.
Channel P&L
1 to 31 August 2026 · margin after landed COGS
Revenue
£97,500
▲ 5.9% on July
Landed COGS
£60,110
incl. freight & duty
Gross margin
38.3%
£37,390 gross profit
Channels
5
reconciled to payouts
| Channel | Revenue | Gross profit | Margin |
|---|---|---|---|
| Shopify | £38,420 | £17,290 | 45.0% |
| Amazon FBA | £28,140 | £8,720 | 31.0% |
| eBay | £15,610 | £5,310 | 34.0% |
| Etsy | £9,170 | £3,760 | 41.0% |
| TikTok Shop | £6,160 | £2,310 | 37.5% |
SKU profitability
August 2026 · per unit, net of VAT
Yoga mat 6mm on Amazon FBA is now at 7.0% margin. Landed cost rose £1.11 a unit after the July shipment's freight increase. Same product on Shopify: 30.7%.
| Product | Channel | Units | Price | Landed cost | Fees & ads | Profit / unit | Margin |
|---|---|---|---|---|---|---|---|
| Yoga mat 6mmYM-6MM-PUR | Amazon FBA | 640 | £20.83 | £11.95 | £7.42 | £1.46 | 7.0% |
| Yoga mat 6mmYM-6MM-PUR | Shopify | 410 | £23.33 | £11.95 | £4.22 | £7.16 | 30.7% |
| Cork block, pairCB-CORK-2 | Shopify | 520 | £12.49 | £3.20 | £2.95 | £6.34 | 50.8% |
| Resistance bands, set of 5RB-SET-5 | Amazon FBA | 880 | £16.66 | £4.10 | £6.38 | £6.18 | 37.1% |
| Foam roller 45cmFR-45 | eBay | 300 | £20.83 | £7.80 | £6.10 | £6.93 | 33.3% |
| Meditation cushionMC-BUCK | Etsy | 190 | £29.16 | £9.40 | £5.20 | £14.56 | 49.9% |
| Water bottle 750mlWB-750 | TikTok Shop | 410 | £12.49 | £4.60 | £2.90 | £4.99 | 40.0% |
Margin bands: under 15% red, 15 to 30% amber, over 30% green.
13-week cash flow forecast
From w/c 7 September 2026
Cash today
£32,200
Lowest point
£18,400
w/c 5 Oct
Cash buffer
£15,000
£3,400 headroom at the low
End of forecast
£89,100
after Q4 stock is paid
Example figures for illustration. Your dashboards are built from your own reconciled data. See it with your numbers.
Pricing
A seller on one Amazon marketplace with up to 500 orders usually starts on Basic. Selling on more than one platform, wanting SKU-level COGS or needing cash flow forecasting moves you to Growth. Multi-currency marketplaces and paid ads reconciliation sit on Scale.
Compliance
£250/mo
Sole trader. £590/mo ltd company.
Basic
£350/mo
Single platform, up to 500 orders.
Growth
£700/mo
Multi-platform.
Scale
£2,500+/mo
Seven-figure operations.
Fractional FD
£4,500+/mo
Everything included.
Keep reading
Amazon, Shopify, eBay and Etsy reconciled into one set of books via A2X.Duty, freight and import VAT built into your cost of goods sold.Marketplace VAT, import VAT and EU sales handled properly.Selling on your own store as well? How we handle Shopify payouts and VAT.
