Shopify Payments
The main payout, covering cards and wallets such as Apple Pay. Reconciled through A2X against each deposit.
Shopify accountant
Shopify Accountants Who Reconcile Every Payout
eCounts is a Shopify accountant for UK stores that want to know what they actually make. We reconcile every payout and payment gateway into Xero or QuickBooks, build real cost of goods sold and get your VAT right, because on Shopify every one of those decisions is yours.
Book a discovery call 
Led by an ICAEW chartered accountant- Shopify, PayPal, Klarna and Clearpay reconciled
- Fixed monthly fee, rolling agreement
In short
eCounts provides specialist accounting for Shopify sellers in the UK. We connect Shopify to Xero or QuickBooks through A2X, reconcile Shopify Payments payouts and other gateways, track true cost of goods sold and handle VAT, including the threshold and cross-border sales. It suits stores whose Shopify dashboard and bank balance no longer tell the same story.
Platforms we reconcile every month
Trademarks belong to their owners. eCounts is independent and not endorsed by these platforms.
The Shopify trap
Why your Shopify dashboard is not your profit and loss
Shopify admin reports orders, not accounts. Its sales figure can include shipping charged to customers, can treat gift card sales as income before anyone redeems them, and records refunds when they happen rather than against the original sale.
It also leaves things out. Gateway fees come off before the money lands, the cost per item field is often empty or out of date, and your apps, theme and ad spend are not in the profit picture at all. The result is a dashboard that can look healthy while the bank says otherwise.
Unlike Amazon, Shopify is not a marketplace collecting tax for you. You are the merchant of record for every sale, gateway, refund and cross-border order. Our Shopify bookkeeping and management accounts start from that reality, with payout and gateway reconciliation underneath and, if you import, landed cost accounting feeding your cost of goods. If you also sell on Amazon, see how we handle Amazon settlements and marketplace VAT.
Shopify payouts
What is inside a Shopify payout
Shopify Payments pays out on a schedule, net of everything deducted in that payout period. This is why the bank never matches the orders, and how each line should land in your accounts.
| Line in the payout | What it is | Where it belongs |
|---|---|---|
| Gross sales | Orders paid through Shopify Payments, including VAT and shipping | Sales and shipping income, VAT separated |
| Processing fees | Card and wallet fees taken before payout | Cost of sales, so gateway fee load is visible |
| Refunds | Money returned to customers, often from a later payout | Against sales, in the period they relate to |
| Chargebacks | Disputed payments reversed, plus a dispute fee | Separate line, so dispute rates are tracked |
| Reserves and adjustments | Funds Shopify holds back or releases | Balance sheet, not income or cost |
| Net payout | The amount that reaches your bank | Matched to the bank deposit exactly |
Payouts from PayPal, Klarna, Clearpay and other gateways follow their own timetables and are reconciled separately.
Free calculator
Shopify profit per order calculator
See what an order earns after VAT, Shopify Payments fees, postage and advertising, and the price you would need for a 30% margin.
Per sale
- Customer pays
- £0.00
- VAT to HMRC
- £0.00
- Platform fees
- £0.00
- Landed cost
- £0.00
- Postage and advertising
- £0.00
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 your Shopify subscription and app costs, which are monthly overheads rather than per-order costs.
Get your real margins checked
Shopify Xero integration
Shopify Xero integration, done properly
The aim is simple: every payout in your bank matched to a journal that explains it, with sales, fees, refunds and VAT in the right accounts.
- 01
Orders and payouts in Shopify
Every order, refund and fee is recorded in Shopify, and each Shopify Payments payout is a bundle of those transactions.
- 02
A2X builds the journal
A2X reads the payout, groups transactions by type and gateway, and creates a summarised journal mapped to your accounts and VAT codes.
- 03
Journal posts to Xero or QuickBooks
One journal per payout lands in your ledger, rather than one invoice per order clogging it up.
- 04
Deposit matches the bank
The net figure equals the bank deposit, so reconciliation is one click, and any gap is flagged rather than buried.
What people try first
Why bank feeds and CSV exports break
Common DIY setups
- Bank feed: posts the net payout as sales, so fees vanish
- CSV exports: manual, error-prone and never quite current
- One invoice per order: thousands of lines, slow to reconcile
- VAT worked out from deposits, not from sales
- Refunds and chargebacks land in the wrong month
Our A2X-based setup
Gross sales, fees and refunds posted separately- Summarised journals that stay readable
- Each journal matches the bank deposit
- VAT coded at the point the journal is built
- Accrual timing that respects month ends
Payment gateways
Reconciling every payment gateway
Most stores take money through more than one route. Each settles on its own schedule, takes its own fees and reports differently.
PayPal
Holds a balance, nets fees and may convert currency. Needs treating as its own bank account, not a sales channel.
Klarna and Clearpay
Buy now, pay later providers pay you in batches, net of their fees, often days after the order. Refunds can be clawed back from later payments.
POS and Stripe
Shopify POS sales in a shop, or a separate Stripe account, add another stream that has to tie back to orders.
Shopify accounting software
Shopify accounting software: Xero, QuickBooks Online and A2X
Shopify is where you sell; it is not an accounting system. Its reports show orders and payouts, but they do not keep double-entry financial records, value your stock or produce financial statements. For that, a Shopify business needs accounting software such as Xero or QuickBooks Online, connected to the store.
We connect Shopify through A2X, which turns each Shopify Payments payout into a summarised entry with sales, refunds, shipping income, payment processing fees and gift cards split out. Other gateways such as PayPal, Klarna and Clearpay are reconciled through their own clearing accounts. The result is accounting and bookkeeping that agree with the bank, ready for accrual accounting, a monthly profit and loss, a balance sheet and a cash flow statement.
Inventory management stays in Shopify or your stock system; we take the stock value from it each month and put cost of goods sold through your accounts, so the margin your Shopify business reports is real.
VAT on Shopify
Shopify VAT: you are the merchant of record
On Shopify no marketplace accounts for VAT on your behalf. Once registered, you charge VAT at the right rate (20% standard, 5% reduced or zero) and account for it on your return, through Making Tax Digital compatible software.
Your Shopify tax settings decide whether prices include VAT. If they do, a sixth of every standard-rated sale goes to HMRC, so registering can cut your margin overnight unless you reprice. Getting rates wrong on zero-rated goods, such as most children's clothes, means overpaying for as long as the setting stays wrong.
Orders shipped from Great Britain to EU customers leave the UK as exports and arrive as EU imports, so customers can face VAT and duty on delivery. Great Britain businesses can use the Import One Stop Shop for low-value consignments, but only through an intermediary. US sales bring state sales tax rules of their own. Our VAT returns and MTD service covers all of it, and importers can use postponed VAT accounting.
Tax
Do I have to pay tax if I sell on Shopify?
Yes, if you are trading. Profit from a Shopify store is taxable like any other business income. Sole traders pay Income Tax and Class 4 National Insurance through Self Assessment once trading income goes over the £1,000 trading allowance. Limited companies pay Corporation Tax on their profits. VAT applies separately, once taxable turnover goes over £90,000 in any rolling 12 months.
Good tax compliance starts with keeping personal and business finances apart: a separate bank account for the store, and every payout, fee and refund recorded in your financial records. That is also what makes Making Tax Digital for Income Tax straightforward for sole traders as the thresholds fall in 2027 and 2028.
Shopify bookkeeping
Shopify bookkeeping: the details that move your margin
Stock and COGS
We build cost of goods sold from landed cost, including freight and duty, and handle variants, bundles and stock at a 3PL.
- Category-level COGS on Basic
- SKU-level COGS on Growth
Apps and subscriptions
App charges arrive on the Shopify bill rather than as separate suppliers. We split them out so you can see what your tech stack costs and cancel what you do not use.
Refunds and chargebacks
Partial refunds, returns and disputes are matched to the original sale, so a high-return month does not distort the next one.
Subscriptions and currency
Subscription stores need deferred revenue and failed payments tracked. Selling in several currencies through Shopify Markets brings exchange differences.
- Multi-currency on Scale
Top tips
Five tips for Shopify store owners
- 01
Reconcile payouts, not orders, to the bank
A Shopify payout bundles many orders, less fees, refunds and chargebacks. Matching each payout to its orders is the only way the bank, the sales figure and the fees all agree.
- 02
Give every payment gateway its own clearing account
PayPal, Klarna, Clearpay and Shopify Payments each settle on their own timetable. Posting each one through its own clearing account shows straight away when money has not arrived.
- 03
Record shipping income and shipping cost separately
Postage charged to customers is income and the courier bill is a cost. Netting them hides whether delivery is making or losing you money.
- 04
Treat unredeemed gift cards as a liability
Money taken for a gift card is not a sale until the card is used. Recording it as revenue straight away overstates income.
- 05
Split your Shopify bill by app
Subscription and app charges arrive on one bill. Splitting them shows what each tool really costs, which makes the annual app review much quicker.
From the accountant
“Shopify's sales figure includes VAT and postage and ignores what your products cost, so it can look healthy while margin shrinks. We reconcile every payout to the bank, so the profit you see is the profit in your accounts.”
Key facts for 2026
Shopify accounting: key facts for 2026
-
2% + 25p is the Shopify Payments online rate for UK cards on the Basic plan, falling to 1.7% + 25p on Shopify and 1.5% + 25p on Advanced.
March 2026. Source: Shopify UK pricing, as summarised by Airwallex (March 2026)
-
£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
-
£1,000 of gross trading income a year can be received tax-free under the trading allowance, without telling HMRC.
2026/27 tax year. Source: GOV.UK, Tax-free allowances on property and trading income
-
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
Changes coming for Shopify stores
What changes for Shopify sellers between now and 2031, with the official source for each.
-
MTD for Income Tax threshold falls to £30,000
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
-
Penalty points for late MTD quarterly updates begin
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.
-
Benefits in kind must go through payroll
Company cars, car fuel, vans, van fuel and employer-provided medical benefits must be reported in real time through payroll, replacing P11D forms for those benefits. Most remaining benefits follow from April 2028.
Source: GOV.UK, Changes to reporting of benefits in kind from April 2027
-
Small companies must file a profit and loss account
Companies House plans to require small and micro companies to file a profit and loss account (with an option to keep it off the public register) and to file accounts through software only.
Source: GOV.UK, Companies House to bring in changes to accounts filing from April 2028
-
MTD for Income Tax threshold falls to £20,000
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
-
EU ends its temporary €3 duty on low-value parcels
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
-
Mandatory e-invoicing for all VAT invoices
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
Find out what your Shopify store really makes
Book a discovery call and we will look at how your payouts, gateways, stock and VAT are handled today, and what would change.
Example dashboards
What your Shopify numbers look like with us
Every payout reconciled, margin by channel and by product, and a cash forecast built from your real sales pattern.
eCounts client dashboard Sample data
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
- Shopify
- Amazon FBA
- eBay
- Etsy
- TikTok Shop
| 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
Which plan fits a Shopify store
A single Shopify store with up to 500 orders usually starts on Basic. Taking payments through several gateways, selling on Amazon or eBay as well, or wanting SKU-level COGS and cash flow forecasting moves you to Growth. Multi-currency stores 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.
- Usual fit
Growth
£700/mo
Multi-platform.
Scale
£2,500+/mo
Seven-figure operations.
Fractional FD
£4,500+/mo
Everything included.
Can you do bookkeeping in Shopify? 
Not fully. Shopify reports show orders and payouts, but they are not a double-entry accounting system and do not produce a balance sheet or value stock. Most Shopify businesses connect the store to Xero or QuickBooks Online for their bookkeeping.
Does Shopify integrate with QuickBooks and Xero?
Yes, through apps. We use A2X to send summarised Shopify Payments payouts to Xero or QuickBooks Online, which keeps the accounts accurate without posting every single order.
Does HMRC check Shopify sales?
HMRC relies on what you report, and can ask banks and payment providers for information when it opens an enquiry. Shopify sales are taxable trading income, so the safest approach is records that reconcile every payout to the bank.
Does Shopify handle my VAT?
No, Shopify calculates tax at checkout based on your settings, but you are responsible for it. You charge, record and pay the VAT to HMRC, so if the settings are wrong the error is yours to correct.
How do I connect Shopify to Xero?
The most reliable Shopify Xero integration uses A2X, which posts a summarised journal for each payout. It separates sales, fees, refunds and VAT and matches the bank deposit, which a bank feed or per-order connector does not.
Why does my Shopify payout not match my sales?
Because payouts are net and run on their own schedule. Processing fees are deducted first, refunds and chargebacks can come out of later payouts, and other gateways pay separately.
When do I have to register for VAT?
When your taxable turnover in any rolling 12 months goes over £90,000, or you expect it to within the next 30 days. In the first case you must register within 30 days of the end of the month you went over.
Is my Xero bank feed enough for Shopify bookkeeping?
No. A bank feed only sees the net payout, so gross sales, fees, refunds and VAT are missing or wrong unless the payout is broken down first.
Is Shopify Payments the same as Stripe?
Not for your accounts. Shopify Payments is reported and paid out by Shopify, while a separate Stripe account has its own balance, fees and payouts that need reconciling on their own.
Do I only need an accountant at year end?
Not if you want to use your numbers to run the business. Monthly reconciliation keeps VAT returns accurate and shows margin problems while you can still act on them.
Keep reading
Related services and guides
- Multi-platform reconciliation
Shopify, Amazon, eBay and Etsy reconciled into one set of books via A2X. - VAT returns and MTDVAT settings, threshold planning and cross-border sales handled properly.
- Amazon accountantsSelling on Amazon too? How we handle settlements, FBA and marketplace VAT.
- Import duty calculatorWork out the landed cost of your next shipment before you price it.