QUICK ANSWER
Xero + Link My Books is the right stack for UK Amazon FBA sellers in 2026. Xero (~£14-39/month) handles bookkeeping and MTD-compliant VAT submission. Link My Books (~£17-55/month) connects Amazon Seller Central to Xero and reconciles every payout into the correct revenue, refund, FBA fee, and VAT entries automatically. QuickBooks works but Link My Books integration is weaker on the QB side. SellerBoard is a profit tracker, not accounting software — use it alongside, not instead of.
What you actually need
UK Amazon FBA bookkeeping has three jobs:
- Reconcile Amazon payouts. Each disbursement is a net of revenue, refunds, fees, advertising, storage. The accounting software needs to break that into proper journal entries — not lump it as a single income line.
- Handle VAT correctly. Sales VAT, input VAT on supplier costs, FBA fees with reverse-charge VAT (Amazon Luxembourg), MTD-compliant submission to HMRC.
- Year-end ready. Companies House filing, P&L, balance sheet, your accountant can pull it without three weeks of cleanup.
Xero + Link My Books: the right stack
Xero
- ~£14-39/month UK pricing depending on tier.
- MTD-compliant VAT submission native.
- Bank feed to your business account.
- UK accountant universally familiar — they all use Xero.
- Cleaner UI than QuickBooks for the FBA use case.
Link My Books
- ~£17-55/month depending on order volume.
- Connects Seller Central to Xero (or QuickBooks).
- Reconciles each Amazon payout into proper revenue, refund, FBA fee, advertising, storage, and VAT entries.
- Handles Amazon's reverse-charge VAT correctly (Amazon Luxembourg invoices for FBA fees).
- Works for amazon.co.uk + multi-marketplace.
- linkmybooks.com
Combined cost
~£31-94/month all-in. Less than the cost of one hour of accountant time per month. Saves your accountant ~5-15 hours per quarter on Amazon reconciliation, which translates to lower fees.
QuickBooks alternative
Workable but second-best. Reasons:
- Link My Books integration is more mature on Xero. QuickBooks integration works but requires more manual category mapping.
- UK accountants are more Xero-fluent. Some still use QuickBooks but the trend is Xero-ward.
- Pricing is similar (~£14-50/month UK).
If you're already on QuickBooks: stay. The migration cost outweighs the marginal benefit. If starting fresh: Xero.
What about SellerBoard?
SellerBoard is a profit tracker, not accounting software. It does daily P&L by SKU brilliantly, but it doesn't handle:
- Companies House submission.
- HMRC VAT submission (MTD-compliant).
- Bank reconciliation (your business account).
- Year-end P&L / balance sheet.
Run SellerBoard alongside Xero + Link My Books, not instead of. SellerBoard tells you which SKUs are profitable; Xero tells HMRC how much VAT you owe.
UK VAT considerations
The UK VAT threshold rose to £90,000 in 2024. Below that you can voluntarily register or stay unregistered. Above it, registration is mandatory within 30 days of crossing.
If voluntarily registered, the Flat Rate Scheme (FRS) is rarely worth it for FBA — your input VAT on FBA fees and supplier costs is usually higher than FRS would let you reclaim. Most UK FBA operators use the standard scheme.
This is a topic where you absolutely need a UK accountant who understands FBA — generic small-business accountants will get the reverse-charge VAT on FBA fees wrong every quarter. See our VAT for Amazon FBA UK guide.
Comparison table
| Stack | Cost/mo | UK FBA fit |
|---|---|---|
| Xero + Link My Books | £31-94 | Excellent |
| QuickBooks + Link My Books | £25-90 | Good |
| QuickBooks alone (manual) | £14-50 | Poor — manual reconciliation |
| FreeAgent | £14-30 | Workable for solo, weak Amazon integration |
| Spreadsheet | £0 | Inadequate above £30K/yr revenue |
The verdict
Xero + Link My Books for UK Amazon FBA. ~£31-94/month all-in, MTD-compliant, your accountant will thank you. Pair with SellerBoard for SKU-level daily profit visibility.
Don't try to run UK Amazon FBA on a spreadsheet above £30K/year revenue. The reverse-charge VAT alone gets too complex, and HMRC penalties for MTD non-compliance are real.
FAQ
What's the best accounting software for UK Amazon FBA in 2026?
Xero plus Link My Books. Xero handles bookkeeping and MTD VAT submission; Link My Books reconciles Amazon payouts into proper journal entries automatically. Combined cost ~£31-94/month.
Can I use QuickBooks for UK Amazon FBA?
Yes, but Xero has better UK accountant adoption and more mature Link My Books integration. If you're on QuickBooks already, stay. If starting fresh, choose Xero.
Is SellerBoard accounting software?
No — SellerBoard is a profit tracker. It does daily P&L by SKU but doesn't handle HMRC VAT submission, Companies House filing, or bank reconciliation. Use it alongside Xero, not instead of.
Do I need an accountant if I use Xero + Link My Books?
Yes — for VAT submission strategy, year-end accounts, Corporation Tax, and dividend planning. The software does the bookkeeping; the accountant does the strategy and submission. Most FBA-fluent UK accountants charge £100-£300/month for this.
How much does Link My Books cost UK?
Roughly £17-55/month depending on Amazon order volume. Tiers scale with monthly transactions. Yearly billing offers a discount.
Can I do UK FBA accounting on a spreadsheet?
Workable below ~£30K/year revenue and only if you're not VAT-registered. Above that, the reverse-charge VAT on FBA fees and the volume of payouts make manual reconciliation error-prone. Move to Xero before crossing the VAT threshold.
Educational content from a live UK Amazon FBA operator. Not financial, legal, or tax advice — talk to a qualified UK accountant for your specifics. Tool features and prices change; check the vendor's site before subscribing.
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