Shopify Payments and Stripe
Shopify payouts and Stripe payouts bundle many orders, net of processing fees, and often span a month end. Each gets its own clearing account so timing differences are visible.
Multi-platform reconciliation
eCommerce Bookkeeping and Multi-Channel Reconciliation
A2X accounting, clearing accounts and payment processor reconciliation, set up and checked by people who do it every month. Every payout is broken back into sales, fees, refunds and VAT, and tied to the penny to your bank in Xero or QuickBooks.
Book a discovery call 
Amazon, Shopify, eBay and Etsy through A2X- Stripe, PayPal, Klarna, Clearpay, Shopify Payments and Square
- Led by an ICAEW chartered accountant
In short
Multi-platform reconciliation is the ecommerce bookkeeping work that turns lump-sum marketplace and processor payouts back into gross sales, each fee type, refunds and VAT, so your accounts match what really happened. eCounts sets up A2X for Amazon, Shopify, eBay and Etsy, connects other channels and payment processors through suitable integrations, and checks every payout against the bank each month.
Works with the platforms and software you already use
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Amazon -
Shopify -
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Etsy -
TikTok Shop -
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Xero -
QuickBooks - A2X
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PayPal -
Stripe -
Klarna
Trademarks belong to their owners. eCounts is independent and not endorsed by these platforms.
The problem
Why your payout is not your sales figure
Amazon, Shopify, eBay and Etsy do not pay you your sales. They pay you a single net amount every few days or every fortnight, after taking selling fees, fulfilment fees, advertising, refunds and sometimes a reserve. If that deposit is posted in Xero as one line of income, every number downstream is wrong: turnover is understated, costs disappear and margin looks better or worse than it really is.
Done properly, each payout is broken back into its parts: gross sales, each fee type, refunds, VAT and the net amount that landed in the bank. The pieces have to add back up to the deposit exactly. That is what "reconciled" means on this page, and it is the foundation for reliable bookkeeping and management accounts and for an accurate VAT return.
The gap compounds. A few unmapped fees a month becomes a margin you cannot trust by year end, and a turnover figure that misleads you near the VAT threshold.
Worked example
One Amazon settlement, gross to net
This is the kind of breakdown A2X produces for a single settlement period. The figures are illustrative only, not from a client.
| Settlement line | Amount | Where it is posted |
|---|---|---|
| Product sales (including VAT) | £10,000.00 | Sales, with VAT split out |
| Refunds to customers | -£450.00 | Refunds, with VAT reversed |
| Referral (selling) fees | -£1,350.00 | Marketplace fees |
| FBA fulfilment fees | -£1,800.00 | Fulfilment costs |
| Advertising charged to the settlement | -£600.00 | Advertising |
| Net payout to bank | £5,800.00 | Clears the Amazon clearing account |
Illustrative figures. The net payout is 58% of gross sales here, which is why posting the deposit as income understates turnover and hides every cost above it.
How it works
Settlement-level posting and the clearing account method
A2X reads each settlement or payout, summarises it by transaction type and posts one balanced entry to Xero or QuickBooks. A clearing account sits in the middle so the bank only ever matches money that has actually arrived.
- 01
The sales and fees are recognised
When a settlement closes, A2X posts the sales, fees, refunds and VAT to the right accounts, dated to the right period.
- 02
The net sits in a clearing account
The balance owed to you is posted to a clearing account for that channel, rather than straight to the bank. It represents money the platform holds on your behalf.
- 03
The bank deposit empties it
When the payout lands, the bank line is matched against the clearing account. If the figures agree, the clearing account returns to zero for that payout.
- 04
Leftover balances get investigated
A balance that does not clear means something is missing, duplicated or held back, such as a reserve or an unmapped fee.
The reconciliation process
The ecommerce reconciliation process in five steps
- 01
Download the settlement
Take the settlement or payout report from each channel, for example your Amazon Seller Central account or Shopify Payments, rather than the bank line.
- 02
Split the transaction data
Break each settlement into sales, refunds, fees, advertising, shipping and VAT, so each one is posted to its own account.
- 03
Post to a clearing account
Post the split settlement to a clearing account for that channel in your accounting software, with a link to the source report for the audit trail.
- 04
Match the payout to the bank
When the payout reaches the bank, match it against the clearing account. A zero balance means every penny is accounted for.
- 05
Review the exceptions
Investigate anything left in a clearing account: reserves, missing payouts or chargebacks. This is where errors are caught before they reach your financial statements.
Two approaches
Settlement-level vs order-level posting
For most sellers we use settlement-level summaries, because they tie to the bank and keep the ledger readable.
Settlement-level (how A2X works)
One summarised entry per settlement or payout- Ties directly to each bank deposit
- Keeps Xero or QuickBooks fast and readable at high order volumes
Order-level
- An invoice or entry for every individual order
- Useful where you need customer-level records in the ledger
- Still needs a separate step to tie orders to payouts
Channel by channel
Amazon Xero integration, Shopify Xero integration and the rest
We are specific about how each channel connects, because the honest answer is not the same for all of them.
| Channel | How it connects | Where a person is still needed |
|---|---|---|
| Amazon | A2X for Amazon, settlement by settlement | New fee types, reserves, multi-marketplace VAT |
| Shopify | A2X for Shopify, split by payment gateway | Gift cards, manual orders, gateway mismatches |
| eBay | A2X for eBay, payout by payout | Promoted listings, postage labels, held funds |
| Etsy | A2X for Etsy, by deposit | Etsy Ads, offsite ads fees, currency conversion |
| WooCommerce | A suitable integration for your setup, alongside the payment processor feeds | More hands-on review than the A2X channels |
| TikTok Shop | A suitable integration where available, with more manual checking | More hands-on review than the A2X channels |
We set up A2X for Amazon, Shopify, eBay and Etsy. WooCommerce and TikTok Shop connect a different way, and we will tell you upfront how much manual work your setup needs.
Payment processors
Shopify payouts, Stripe, PayPal and buy now pay later
Each processor nets off its own fees and pays on its own timetable.
PayPal
PayPal acts as both a payment gateway and a wallet that can hold a balance, pay suppliers and convert currency. We treat it like a bank account in Xero so every movement is accounted for.
Klarna and Clearpay
Buy now pay later providers pay you upfront, less their fee, while the customer pays them in instalments. Refunds and adjustments arrive later and need matching back to the original sale.
Square
Common for sellers with markets or a shop. Card takings settle net of fees and need matching to the right channel, not lumped in with online revenue.
Software
Ecommerce accounting software: what you actually need
Most ecommerce businesses need three layers of bookkeeping software. First, accounting software such as Xero or QuickBooks, where your financial data lives. Second, a connector that brings settlement data in automatically: A2X for Amazon, Shopify, eBay and Etsy, and dedicated integrations for other channels. Third, a process: someone who checks the clearing accounts, deals with the exceptions and closes each month.
Done this way, ecommerce payment reconciliation removes almost all manual data entry and saves hours each month, and the Xero dashboard shows cash flow you can trust. Done without the third layer, software alone posts errors faster. Our management accounts service builds on the reconciled data to show your business's financial health each month.
Where automation stops
What A2X does, what it does not do, and what we add
A2X is very good at one job: turning a marketplace settlement into a correct, balanced accounting entry. It does not decide how your chart of accounts should be built, it does not know your landed cost, and it cannot tell you that a fee Amazon introduced last month has been mapped to the wrong account. Those are judgement calls, and they are what we are for.
Refunds and chargebacks are the usual weak point. A refund can land in a later settlement than the sale, a chargeback can arrive weeks after the payout, and a reimbursement for lost stock can look like a sale if nobody checks. We review clearing account balances every month, follow up anything that does not clear, and fix the mapping so it does not happen again.
If you import, the cost side matters as much as the sales side. We bring landed cost into your cost of goods sold so the margin you see per channel reflects freight and duty, not just the supplier price. Platform-specific detail lives on our Amazon accountants and Shopify accountants pages.
Example dashboards
What reconciled data gives you
Once every settlement and payout is reconciled, revenue, fees and margin by channel and product come straight out of your books.
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.
Example figures for illustration. Your dashboards are built from your own reconciled data. See it with your numbers.
Key facts for 2026
Why ecommerce reconciliation matters in 2026
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28.8% of all retail sales in Great Britain were made online in August 2026, up from 28.4% in July.
August 2026. Source: ONS, Retail sales, Great Britain: August 2026
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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
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£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
Figures checked 9 October 2026. Rates and thresholds change, so check the source before relying on them.
Stop guessing what each channel really makes
Tell us which platforms and processors you use and we will show you how they would connect, and where the manual work sits.
Top tips
Four reconciliation tips
- 01
Never post a payout as a sale
A payout is sales less fees, refunds and reserves. Posting it as revenue understates sales and hides costs.
- 02
Use a clearing account for every channel
Each marketplace and gateway gets its own clearing account. When a payout lands, the clearing account should return to zero.
- 03
Reconcile every month, not at year end
A month of settlements takes minutes to check while it is fresh. A year of them takes days and still leaves questions.
- 04
Check reserves and held funds
Marketplaces sometimes hold back part of a payout. Tracking those reserves stops cash in transit being lost in the books.
Pricing
Reconciliation is included in every ecommerce plan
Basic covers single-platform reconciliation through A2X. Growth adds multi-platform and payment processor reconciliation.
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.
What is the best accounting software for an ecommerce business? 
For most UK online sellers it is Xero or QuickBooks, paired with a connector such as A2X that summarises each settlement. The right choice depends on your channels, your accountant and whether you need multi-currency, so there is no single best option.
Can AI tools like ChatGPT do my bookkeeping?
Not on their own. AI tools can help categorise transactions and draft explanations, but reconciling settlements to the bank, valuing stock and getting VAT right still needs accounting software, a proper process and someone accountable for the figures.
What is online bookkeeping?
Online bookkeeping means keeping your records in cloud accounting software, fed automatically from your bank and sales channels, with your bookkeeper or accountant working on the same live file.
Why does my payout not match my sales?
Because the payout is your sales minus everything the platform has deducted. Selling fees, fulfilment fees, advertising, refunds and any reserve are taken before the money reaches you, and a single payout can cover orders from different days or months. Reconciliation breaks the payout back into those parts so both figures make sense.
What is A2X?
A2X is software that connects Amazon, Shopify, eBay, Etsy and other channels to Xero or QuickBooks and posts each settlement as a summarised, balanced accounting entry. It splits out sales, fees, refunds and VAT and uses clearing accounts so each entry can be matched to the bank deposit. We set it up and maintain the mappings for Amazon, Shopify, eBay and Etsy.
How do I connect Amazon to Xero?
The most reliable way is through A2X rather than a bank feed alone. A2X reads each Amazon settlement and posts it to Xero with fees, refunds and VAT on the right accounts, then the deposit is matched to a clearing account. We handle the setup, the account mapping and the monthly checks.
Is the Shopify Xero integration enough on its own?
Usually not for accurate accounts. A basic Shopify Xero integration can push orders across, but it does not tie each payout to the bank with fees separated. A2X for Shopify splits activity by payment gateway so each one reconciles.
Will I still need a bookkeeper?
Not a separate one. Reconciliation sits inside our ecommerce bookkeeping service, so the same team maps the platforms, reviews the clearing accounts and prepares your monthly figures and VAT return.
What happens if I add a new sales channel?
We connect it and map it before its first payout is posted. If it is Amazon, Shopify, eBay or Etsy, that means adding it to A2X. Other channels need the right integration for that platform, and we will tell you upfront how much manual review it involves.
Keep reading
Related services and guides
- Bookkeeping and management accounts
Monthly figures and SKU-level margins built on reconciled data. - VAT returns and MTDReturns prepared from reconciled channel data, not bank deposits.
- eBay accountantsHow eBay payouts, promoted listings and postage fit together.
- Etsy accountantsEtsy deposits, ads fees and currency conversion explained.