If you sell on Amazon in the UK, you've probably stared at a settlement report and wondered how on earth it turns into a clean VAT return. A2X and Link My Books are the two tools most accountants reach for to fix that. Both take the raw payout data and post tidy, reconciled journals into your bookkeeping software.
So which one should you use? That's what this guide is for.
We use both in practice at Zmartly, depending on the client. This is an independent comparison, not an affiliate pitch. We'll look at how each handles UK and EU VAT, how the reconciliation actually works, what they cost in broad terms, and where each one shines. We'll also walk through a worked Amazon settlement so you can see what "good" looks like in your accounts.
This is written for UK sellers and the figures relate to the 2025/26 tax year.
What do A2X and Link My Books actually do? {#what-do-they-do}
Both tools sit between Amazon and your accounting software (typically Xero or QuickBooks). They read each Amazon settlement, split it into its components, and post a single summarised, VAT-coded journal that reconciles to the exact penny that lands in your bank.
In short, they turn one messy lump payout into clean, reconcilable bookkeeping. That's the whole job, and both do it well. The differences are in the detail of how, and how much hand-holding you get.
Neither tool files your VAT return or talks to HMRC directly. They feed accurate numbers into your bookkeeping software, which is where your Making Tax Digital (MTD) VAT return is then prepared and submitted. MTD for VAT is mandatory for all VAT-registered businesses, so your records must be kept digitally and returns filed through compatible software (gov.uk).
Why can't I just use the Amazon payout figure? {#why-not-payout}
This is the single most common mistake we see, and it's why these tools exist.
The amount Amazon pays into your bank is net of everything: selling fees, FBA fees, advertising, refunds, reserves and any VAT Amazon has collected on your behalf. If you record that net payout as your sales, your turnover is understated, your expenses are invisible, and your VAT is wrong.
Your VAT-taxable turnover is your gross sales, not your net payout. That matters because the UK VAT registration threshold is £90,000 of taxable turnover (current, from 1 April 2024), and it's measured on a rolling 12-month basis (gov.uk). Reconcile from the net payout and you can sail past £90,000 without realising it.
A2X and Link My Books both solve this by exploding the settlement back out into gross sales, separate fee lines, refunds and VAT, so your books show the real picture.
How do they handle UK VAT? {#uk-vat}
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Both tools let you map each transaction type to a VAT rate and a nominal account. Standard-rated UK sales get coded at 20%, zero-rated goods (such as most books and children's clothing) at 0%, and so on (gov.uk).
The practical difference is the default setup. Link My Books leans towards a guided, wizard-style setup with pre-built VAT mappings aimed at sellers who don't have an accountant configuring it for them. A2X is more of a blank canvas: extremely flexible, but it assumes whoever sets it up knows which VAT rate belongs on which line.
In our experience, that's the real fork in the road. If an accountant is doing your setup, A2X's flexibility is a strength. If you're a hands-on seller doing it yourself, Link My Books' guardrails reduce the chance of mis-coding a line.
Both correctly separate the fees Amazon charges you. Since 1 August 2024, Amazon charges UK VAT on most seller fees to UK-established sellers (rather than the previous reverse-charge treatment from Luxembourg), so those fee lines now carry UK input VAT you can reclaim through your VAT return. Both tools handle this, but the mapping must be reviewed after that change, because an old setup may still be applying the reverse charge.
How do they handle the marketplace deemed-supplier rules? {#deemed-supplier}
This is where UK Amazon VAT gets genuinely tricky, and where the quality of your reconciliation tool earns its keep.
Since 1 January 2021, where goods are sold through an online marketplace such as Amazon, the marketplace is treated as the deemed supplier and is liable to account for the UK VAT in two situations:
- Consignments of £135 or less that are located outside the UK at the point of sale and sold to a UK customer. UK supply VAT is charged at the point of sale, and the online marketplace accounts for it (gov.uk).
- Goods of any value that are already located in the UK at the point of sale but sold by an overseas seller through the marketplace. The marketplace is again deemed to be the supplier and accounts for the VAT (gov.uk).
There's a B2B exception: where a UK VAT-registered business customer provides its VAT number, responsibility shifts to that customer under the reverse charge (gov.uk).
For most UK-established sellers holding their own stock in UK FBA warehouses, the deemed-supplier rules don't apply, so you account for your own output VAT as normal. But if you're an overseas seller, or you hold stock abroad and dropship low-value consignments, Amazon collects "Marketplace Facilitator VAT" on those orders. Your reconciliation has to record that VAT as collected-and-remitted-by-Amazon, not as your own output VAT, or you'll double-count it.
Both A2X and Link My Books isolate this marketplace-collected VAT as a distinct line. The point to understand as the business owner is that the tool only codes it correctly if it's been told which of your sales fall under the deemed-supplier rules. Neither tool can guess your establishment status or where your stock sits. That's a setup decision, and getting it wrong is the most expensive mistake in this whole area.
What about EU VAT, imports and PVA? {#eu-vat-pva}
If you sell into the EU or import stock, the reconciliation gets another layer.
For imports of goods into Great Britain, most VAT-registered businesses use Postponed VAT Accounting (PVA). Instead of paying import VAT at the border and reclaiming it later, you account for it on your VAT return (gov.uk). On the return, postponed import VAT goes in:
- Box 1: the import VAT due for the period.
- Box 4: the same import VAT reclaimed (if fully recoverable).
- Box 7: the net value of the imported goods (gov.uk).
The figures come from your monthly online postponed import VAT statement (gov.uk).
Here's the honest limitation: neither A2X nor Link My Books reconciles your import VAT or PVA statements for you. They work from Amazon settlement data, not from your customs declarations. PVA entries are a separate adjustment your bookkeeper or accountant posts using the HMRC statement. Don't expect either tool to handle the import side.
On the sales side, both tools can split EU sales by country and destination, which matters if you store stock across EU fulfilment centres (Pan-EU FBA) and have local VAT registrations. Link My Books markets a strong focus on multi-country VAT mapping out of the box; A2X handles it through its grouping and tax-rate logic. Either works, but multi-country EU VAT is the area where we'd always recommend an accountant reviews the mapping rather than trusting a default.
A2X vs Link My Books: feature comparison {#feature-comparison}
The table below summarises how the two compare on the points that matter most to UK Amazon sellers. This reflects how we use both tools in practice; always check the current feature set, as both products evolve.
| Feature | A2X | Link My Books |
|---|---|---|
| Core job | Summarised settlement journals into Xero / QuickBooks | Summarised settlement journals into Xero / QuickBooks |
| Setup style | Flexible, accountant-friendly, fewer guardrails | Guided wizard, pre-built VAT mappings |
| UK VAT coding | Full control over rates and accounts | Guided defaults plus manual override |
| Marketplace-collected VAT | Isolated as a separate line | Isolated as a separate line |
| Multi-country EU VAT | Handled via grouping and tax rules | Strong out-of-the-box country mapping |
| COGS / inventory | Cost-of-goods tracking available | Cost-of-goods tracking available |
| Multi-channel (eBay, Shopify, Etsy) | Yes | Yes |
| Import VAT / PVA | Not handled (posted separately) | Not handled (posted separately) |
| Best suited to | Accountant-managed setups, larger or complex sellers | Self-serve sellers wanting guardrails |
Illustrative example: one Amazon settlement, posted properly {#worked-example}
Illustrative example. Meet Sana, a UK-established sole trader selling homeware through Amazon UK with her own stock in a UK FBA warehouse. She's VAT-registered. One fortnightly settlement pays £6,420 into her bank. Here's what a tool like A2X or Link My Books unpicks behind that single figure.
All sales below are standard-rated at 20% and are Sana's own supplies (not deemed-supplier sales), so she accounts for the output VAT.
| Settlement component | Net | VAT (20%) | Gross |
|---|---|---|---|
| Product sales | £8,000.00 | £1,600.00 | £9,600.00 |
| Refunds to customers | -£500.00 | -£100.00 | -£600.00 |
| Amazon selling and FBA fees | -£1,800.00 | -£360.00 | -£2,160.00 |
| Advertising fees | -£350.00 | -£70.00 | -£420.00 |
| Net to bank | £6,420.00 |
Check the cash: £9,600.00 gross sales, minus £600.00 refunds, minus £2,160.00 fees, minus £420.00 advertising = £6,420.00. That ties to the bank exactly.
Now the VAT impact for the period from this one settlement:
- Output VAT on sales (Box 1): £1,600.00 less £100.00 on refunds = £1,500.00.
- Input VAT to reclaim (Box 4): £360.00 on fees plus £70.00 on advertising = £430.00 (this assumes Amazon charged UK VAT on the fees, as it does for UK-established sellers from 1 August 2024).
- Net VAT effect of this settlement: £1,500.00 - £430.00 = £1,070.00 payable.
And the profit-and-loss view:
- Net turnover recognised: £8,000.00 - £500.00 = £7,500.00.
- Costs recognised: £1,800.00 fees + £350.00 advertising = £2,150.00.
Notice what would have gone wrong if Sana had simply booked the £6,420.00 payout as sales. Her turnover would be understated by £1,080.00 (£7,500.00 minus £6,420.00), her £2,150.00 of allowable costs would vanish, and her output and input VAT would both be missing. Over a year of fortnightly settlements, that error compounds fast, and it's exactly how sellers accidentally breach the £90,000 threshold without noticing. This is the work A2X and Link My Books automate.
What do they cost? {#pricing}
Both tools price on a tiered subscription, usually billed monthly or annually, with the tier set by your order volume across connected channels. Entry tiers suit low-volume sellers and the price steps up as your monthly order count grows. Multi-channel and multi-country usage typically pushes you into higher tiers.
We're deliberately not quoting specific prices here, because both vendors change their plans regularly and any figure would be out of date quickly. Check each vendor's current pricing page before deciding, and compare on your actual monthly order volume rather than the headline entry price.
In practice, the subscription cost is rarely the deciding factor. The cost of getting your VAT wrong, or of an accountant untangling a year of mis-posted settlements, dwarfs the difference between the two tools' price tiers.
Which one should you choose? {#which-one}
Both are genuinely good tools. Here's our practical steer.
Choose Link My Books if you're a hands-on seller setting it up yourself and you want guardrails. The guided VAT mapping and wizard-style onboarding reduce the chance of a self-build error, which is the most common way DIY setups go wrong.
Choose A2X if you have an accountant managing your books, or you're a larger or more complex seller (multi-channel, Pan-EU, custom nominal structures). Its flexibility is a real advantage when someone who knows VAT is doing the configuration.
Honestly, though, the tool matters less than the setup. We've seen clean books on both and a mess on both. The deciding factors are whether your establishment status and stock locations are correctly reflected in the VAT mapping, whether marketplace-collected VAT is isolated, and whether someone reviews the output each quarter. That's the part we handle for Amazon FBA sellers at Zmartly, regardless of which tool sits underneath.
If you'd rather not gamble on a default mapping, our bookkeeping service sets up and reviews A2X or Link My Books for you, and our tax advisory team handles the establishment and deemed-supplier questions that the software can't answer on its own.
Want your Amazon VAT done right?
Book a free 20-minute call with a Zmartly accountant. We'll review your current Amazon settlement setup, tell you whether A2X or Link My Books fits better, and make sure your VAT coding is correct before HMRC does it for you. Talk to a Zmartly accountant.
FAQs {#faqs}
Is A2X or Link My Books better for UK VAT?
Both handle UK VAT well. Link My Books offers more guided, pre-built VAT mappings that suit sellers configuring it themselves, while A2X offers more flexibility that suits accountant-managed setups. The accuracy depends far more on a correct setup than on which tool you pick.
Do A2X and Link My Books file my VAT return with HMRC?
No. Neither tool files your VAT return or connects to HMRC directly. They post reconciled, VAT-coded journals into your accounting software (such as Xero or QuickBooks), and your MTD-compatible software is what submits the return to HMRC.
Why can't I just record the Amazon payout as my sales?
Because the payout is net of fees, refunds, advertising and any VAT Amazon collected. Recording it as sales understates your turnover, hides your costs and gets your VAT wrong. Your VAT-taxable turnover is your gross sales, which is what matters for the £90,000 registration threshold.
Do these tools handle import VAT and PVA?
No. A2X and Link My Books reconcile Amazon settlement data, not your customs declarations. Postponed VAT Accounting entries (Box 1, Box 4 and Box 7 on your VAT return) are posted separately by your bookkeeper or accountant using your monthly HMRC postponed import VAT statement.
Which tool is best for Pan-EU FBA sellers?
If you store stock across EU fulfilment centres and hold local VAT registrations, both can split sales by country, but this is where mistakes are most costly. We'd always recommend an accountant reviews the multi-country VAT mapping rather than relying on either tool's defaults.
Can I switch from one tool to the other?
Yes. Both connect through your accounting software, so switching mainly means reconnecting and rebuilding your VAT and nominal mappings. The bigger task is making sure the new mapping matches the old one so your historical and future periods stay consistent.
