TITLE: Q4 Compliance and Margin Checks: Your 7 September 2026 To-Do List for Amazon and Shopify Sellers
For the week commencing 7 September 2026, UK Amazon and Shopify sellers should focus on one priority: complete your Q4 compliance and margin checks before peak trading begins.
September is the final practical window to reconcile your accounts, verify VAT positions, review inventory locations and model the additional cost of holiday fulfilment.
1. Plan for Amazon’s Q4 peak fees before you commit to stock
Amazon has confirmed that holiday peak fulfilment fees will apply from 15 October 2026 to 14 January 2027 across relevant FBA, Remote Fulfilment, Multi-Channel Fulfilment and Buy with Prime services.
Amazon expects the increase to average approximately $0.32 per unit, before the existing 3.5% fuel and logistics surcharge. Monthly storage rates will also increase from 1 October.
These costs can materially change your contribution margin. A product that appears profitable using standard fulfilment rates may become marginal once you include:
- Peak fulfilment fees.
- The fuel and logistics surcharge.
- Monthly storage.
- Advertising spend.
- Promotional discounts.
- Refunds and return costs.
- Currency conversion and payment fees.
Create a peak-season SKU model now. For each product, record:
- Selling price.
- Product and packaging cost.
- Amazon referral fee.
- Standard and peak fulfilment fee.
- Storage cost.
- Advertising cost per unit.
- Expected refund or return rate.
- VAT and other transaction taxes.
- Net contribution after all costs.
For example, if a product generates £12 of contribution before peak fees but loses £2.50 through additional fulfilment, storage and advertising costs, your Q4 cash-flow plan must reflect the lower figure.
An Amazon FBA accounting UK workflow should connect settlement data, inventory movements and SKU-level costs. This gives you a more reliable view than reviewing Amazon deposits alone.
Amazon’s official 2026 fulfilment fee guidance should be checked alongside the rate card for your specific marketplace and product size tier.
2. Ship September inventory before the Prime event deadlines
Amazon’s published 2026 inbound deadlines are approaching quickly.
For Prime Big Deal Days:
- 9 September: FBA shipments using minimal shipment splits.
- 16 September: FBA shipments using Amazon-optimised shipment splits.
For Black Friday Week and Cyber Monday:
- 21 October: FBA shipments using minimal shipment splits.
- 28 October: FBA shipments using Amazon-optimised shipment splits.
These dates relate to Amazon’s published Seller Central requirements and may vary by marketplace or fulfilment programme. Confirm your own shipment plan directly in Seller Central.
Before releasing inventory, check:
- Purchase order quantities.
- Supplier production and dispatch dates.
- Freight lead times.
- Customs clearance.
- FBA appointment availability.
- Remaining sellable stock.
- Expected Q4 sales velocity.
- Cash tied up in inbound inventory.
Do not rely only on your bank balance. Inventory purchased for Q4 may not convert into cash until weeks after delivery, especially where Amazon settlement timing, returns and advertising spend overlap.
Our international compliance guide provides useful background for businesses selling across multiple markets.
3. Reconcile Amazon settlements to gross sales
A bank deposit is not the same as revenue.
Amazon may deduct fulfilment fees, referral fees, refunds, advertising, storage, reimbursements, reserves and other charges before paying you. Your bookkeeping should reconcile the full settlement period, not simply post the net deposit as sales.
Complete this weekly reconciliation:
- Match gross orders to Amazon settlement reports.
- Separate sales, refunds and promotional discounts.
- Identify VAT collected or adjusted.
- Post Amazon fees to the correct expense accounts.
- Review reimbursements and damaged-stock claims.
- Match the final settlement figure to your bank statement.
- Investigate unexplained differences before they accumulate.
This is the foundation of accurate ecommerce bookkeeping UK businesses need before filing VAT returns, preparing management accounts or assessing Q4 performance.
Shopify sellers should follow the same principle. Your Shopify payout is a settlement, not a complete accounting record. Reconcile gross orders, payment processing fees, refunds, chargebacks, shipping income and tax collected.
A specialist Shopify accounting UK process should also distinguish domestic sales from overseas transactions and identify where marketplace or payment-provider reports do not match your accounting software.
4. Check your rolling UK VAT turnover
The UK VAT registration threshold remains £90,000 of taxable turnover, tested on a rolling 12-month basis.
It does not reset at the end of your financial year. Review the previous 12 months every month and also consider whether you expect to exceed the threshold in the next 30 days.
Use HMRC’s VAT registration guidance to confirm the current rules and registration deadlines.
Your September review should include:
- Amazon direct sales.
- Shopify sales.
- Wholesale or B2B sales.
- Shipping and other taxable income.
- Refunds and credit notes.
- Marketplace facilitator arrangements.
- Sales made through overseas channels.
- Taxable and exempt supplies, where relevant.
Do not use net Amazon settlements to assess your position. Start with the correct taxable turnover figures before deductions.
If you are VAT-registered, keep your records digitally and file through MTD-compatible software. HMRC’s VAT Notice 700/22 explains the digital record and filing requirements.
5. Review Shopify Tax settings for new stores
For new UK Shopify stores opened on or after 13 May 2026, Basic Tax is no longer available. Sellers must use either Shopify Tax or manual tax settings.
Shopify Tax can support tax calculations, product tax categories and VAT-related reporting data. Manual settings provide more control but require you to maintain rates, product treatment and regional settings accurately.
Whichever option you use, remember that Shopify does not file your VAT returns for you. You remain responsible for:
- Registering for VAT where required.
- Applying the correct VAT treatment.
- Maintaining digital records.
- Reconciling tax collected.
- Preparing and submitting VAT returns.
- Paying HMRC by the relevant deadline.
Review the official Shopify UK tax guidance before changing your settings.
