Why e-commerce accounting is different
Selling online is nothing like issuing invoices with 30-day terms to a handful of B2B clients. A Swiss e-commerce business generates hundreds or thousands of micro-transactions per day, each with its own payment gateway collection, its own commission, any discounts or coupons applied, and a real risk of returns. Traditional accounting — designed for few, high-value invoices — simply cannot handle these volumes without automation.
In Switzerland, VAT rules (LTVA) also apply to B2C online sales: every transaction must be documented, the correct rate applied, and the taxable base calculated net of discounts and vouchers. On top of this, gateway settlement (Stripe pays at T+2, PayPal at T+1, Twint at T+1) creates a time gap between the sale and the actual bank credit — a nightmare to reconcile manually.
This guide covers the specific accounting aspects of Swiss e-commerce: from the differences between B2C and B2B, to the order-to-cash flow, through to managing discounts, returns, commissions and multi-channel reconciliation. The goal is to take you from checkout to balance sheet without errors — with minimal manual effort thanks to AccountEX.
B2C vs B2B accounting: key differences
The accounting for a B2C e-commerce operation differs profoundly from a traditional B2B business. Understanding these differences is the first step to setting up correct processes:
| Aspect | B2C e-commerce | Traditional B2B |
|---|---|---|
| Invoice type | Receipt / simplified QR-invoice per order, often without complete customer data | Nominal invoice with VAT number, payment terms and order reference |
| VAT handling | VAT included in the price shown to consumers (gross → net); rate 8.1% or 2.6% for essential goods | VAT shown separately on invoice; reverse charge possible for EU clients |
| Payment timing | Immediate payment (card, Twint, PayPal) with gateway settlement at T+1 / T+2 | Payment at 30–60 days by QR-bill or bank transfer |
| Returns and refunds | Frequent (5–15% of revenue); require automatic credit notes and VAT adjustments | Rare; handled with formal credit note and commercial agreements |
| Currency | Predominantly CHF; EUR for cross-border or EU customers; automatic gateway conversion | CHF or EUR at agreed rate; exchange differences booked at period end |
| Transaction volume | Hundreds/thousands per day; impossible to record manually | Tens per month; manageable even with semi-manual entry |
The order-to-cash flow: 5 steps
In online commerce, money passes through several intermediaries before reaching your bank account. Here is the complete flow and the accounting implications of each step:
Customer order
The customer completes checkout and the system creates an order with gross amount (price + VAT), any discounts applied, and chosen payment method. In accounting: no revenue is recorded yet, just a commitment (confirmed order). With AccountEX, the order imported from Shopify/WooCommerce automatically generates a provisional entry.
Payment capture
The payment gateway (Stripe, PayPal, Twint) authorises and captures the payment. The amount is now 'in transit' at the gateway. Accounting records a receivable from the gateway (e.g. account 1105 'Stripe Receivables') and gross revenue. VAT is calculated on the taxable base net of discounts.
Gateway settlement
The gateway groups the day's transactions and prepares the payout. Stripe: settlement at T+2 (Switzerland); PayPal: T+1; Twint: T+1 (next business day). At this stage the gateway withholds its commissions. The settlement report is the key document for reconciliation.
Payout to bank account
The net amount (sales – commissions – refunds) is credited to the company's bank account. The accounting entry closes the gateway receivable and records the commission cost (e.g. account 6840 'Bank and gateway commissions'). AccountEX imports the payout via CAMT.054 and reconciles it automatically.
Bank reconciliation
The bank transaction is matched to the gateway payout and to individual orders. Any differences (rounding, currency conversions, chargebacks) are identified and booked. With AccountEX, reconciliation is automatic: the system matches bank CAMT.053, gateway reports and e-commerce orders in a single flow.
Discounts, coupons and VAT: how to handle them
VAT treatment of discounts and coupons is one of the trickiest aspects of e-commerce accounting. Swiss rules (LTVA art. 24) require that the taxable base equals the amount actually paid by the customer:
Percentage discounts and promotions
A 20% discount on a CHF 100 product reduces the taxable base to CHF 80. VAT is calculated on CHF 80, not CHF 100. Correct booking: net revenue CHF 80, VAT 8.1% on CHF 80 = CHF 6.48. Never record revenue at CHF 100 with a separate discount debit — the FTA wants the net taxable base.
Fixed-value coupons
A CHF 15 coupon on a CHF 120 order reduces the taxable base to CHF 105. Note: if the coupon is funded by a partner (e.g. marketplace), the VAT taxable base remains CHF 120, because the customer received CHF 120 of commercial value — the coupon is a partner contribution, not a price reduction.
Gift cards and prepaid vouchers
The sale of a gift card is not subject to VAT at the time of issue (art. 24 para. 6bis LTVA): VAT applies only at redemption, when the voucher is used to purchase goods or services. The voucher is booked as a liability (debt to customer) until redeemed.
Conditional free shipping
If you offer free shipping above CHF 80, the shipping cost is not a discount but an operating cost borne by the company. The VAT taxable base does not change. The shipping cost incurred is recorded in account 4400 'Transport and shipping costs'. If you charge shipping, it is subject to the standard VAT rate (8.1%).
Warning: gift cards sold in your shop do NOT generate VAT revenue at the time of sale. VAT applies ONLY when the card is redeemed to purchase a product. Booking VAT on the gift card sale is an error that the FTA penalises during audits. Use a dedicated liability account (e.g. 2030 'Gift cards to be redeemed').
Returns, refunds and accounting adjustments
Returns are a natural part of e-commerce (Swiss average: 8–12% in fashion, 3–5% in electronics). Every return has precise accounting implications that must be handled correctly:
Full return with refund
The customer returns the entire order. A credit note is issued reversing the revenue and corresponding VAT. The refund is processed through the same gateway as the original payment (Stripe Refund, PayPal Reversal). Accounting: revenue reversal + VAT reversal + reduction of gateway receivable/payable. AccountEX generates the credit note automatically from the Shopify return.
Partial refund
The customer keeps part of the order and is refunded only for the returned items. The credit note covers only the returned items, with proportional VAT. Important: verify that the VAT rate matches the original item (8.1% vs 2.6% for food). The gateway retains the original commission — the commission cost on the refunded amount is not returned.
Exchange / product swap
The customer returns a product and receives another. If the value is identical, only the inventory movement is recorded with no impact on revenue or VAT. If the value differs, a credit note is issued for the return and a new invoice for the replacement item. Watch for VAT rate differences if the items belong to different categories.
Return with restocking fee
If you apply a restocking fee (e.g. 15% of value), the refund is partial. The restocking fee is service revenue subject to 8.1% VAT. Booking: credit note for the full product amount, separate invoice for the restocking fee, net refund to customer via gateway.
Chargebacks and disputes
The customer disputes the payment directly with the bank/card issuer. The gateway withholds the disputed amount plus a chargeback fee (e.g. Stripe: CHF 15 per chargeback). Accounting: record the disputed debt, the extra fee, and if you lose the dispute, the definitive revenue reversal. It is essential to keep shipping documentation as evidence for disputes.
Payment gateway commissions
Every payment gateway withholds a commission on transactions. These commissions must be correctly booked as operating costs. Here is an overview of the main gateways used in Swiss e-commerce:
| Gateway | Typical commission | Booking method | VAT treatment |
|---|---|---|---|
| Stripe | 2.9% + CHF 0.30 per transaction (EU cards); 1.5% + CHF 0.30 for CH cards | Net recording from settlement report; commission to account 6840. Payout at T+2 | VAT exempt (financial service art. 21 para. 2 no. 19 LTVA). No input tax deduction |
| PayPal | 2.99% + CHF 0.55 (domestic sales); 3.49% + fixed fee for cross-border | PayPal balance as transit account (1106). Manual or automatic payout at T+1 | VAT exempt. Cross-border commissions are also exempt as financial services |
| Twint | 1.3% per transaction (no fixed fee); ideal for micro-payments in CHF | Daily settlement T+1 via acquirer (Worldline/SIX). Recording from daily report | VAT exempt. Commission is withheld by the acquirer in the daily settlement |
| PostFinance Checkout | 1.5–2.5% depending on volume; includes PostFinance Card and TWINT | Settlement to PostFinance account with transaction detail. Reconciliation via CAMT.054 | VAT exempt. PostFinance provides a monthly commission summary deductible as a cost |
Multi-channel reconciliation
If you sell on Shopify, Amazon, your own website and perhaps even in a physical shop, reconciliation becomes the accounting bottleneck. Each channel has its own reports, settlement timelines and commissions. Here is how to manage it all efficiently:
Data centralisation
Import all orders from every channel (Shopify, Amazon Seller Central, WooCommerce, POS) into a single accounting system. AccountEX supports automatic import from all major Swiss e-commerce platforms and marketplaces, creating a unified sales view.
Account mapping per channel
Assign a revenue sub-account and a gateway transit account for each sales channel (e.g. 3200.01 'Shopify Revenue', 3200.02 'Amazon Revenue', 1105.01 'Stripe Shopify Receivables', 1105.02 'Amazon Pay Receivables'). This enables profitability analysis by channel.
Settlement vs orders reconciliation
For each gateway payout, verify that the sum of orders included in the settlement matches the amount credited net of commissions and refunds. AccountEX performs this matching automatically, flagging discrepancies.
Marketplace commission management
Amazon withholds a referral fee (8–15%) and an FBA fee if you use Amazon logistics. These must be booked separately from payment gateway commissions. Use dedicated accounts (e.g. 6841 'Marketplace commissions').
Currency conversions
If you sell in EUR on Amazon.de or accept EUR payments on Shopify, conversions generate exchange differences. Book at the transaction-day rate and record exchange differences at month-end (account 6960 'Exchange differences'). AccountEX imports daily ECB rates automatically.
Multi-channel monthly close
At month-end, verify that total revenue per channel + commissions + refunds = total bank movements. This reconciliation is proof that the accounting is correct. AccountEX generates a multi-channel reconciliation report highlighting any residual differences.
Tip: with AccountEX you can automatically import orders from Shopify, WooCommerce and Amazon, reconcile them with gateway payouts and bank CAMT.053 transactions, and get an always up-to-date balance sheet with no manual entries. Average monthly reconciliation time drops from 2 days to 15 minutes.
7 practical tips for e-commerce accounting
- Automate order imports from your online shop (Shopify, WooCommerce) into your accounting software. Manually recording hundreds of transactions per day is unsustainable and error-prone — AccountEX does it automatically
- Create a dedicated transit account for each payment gateway (Stripe, PayPal, Twint). This lets you reconcile payouts with individual transactions and immediately spot any discrepancies
- Always record revenue net of discounts and coupons, never gross with a separate discount entry. The FTA during VAT audits verifies that the taxable base matches the amount actually collected from the customer
- Automate credit notes for returns: every return must automatically generate a credit note with the corresponding VAT reversal. With AccountEX, a return imported from Shopify generates the credit note in one click
- Reconcile gateway payouts at least weekly, not just at month-end. Discrepancies accumulate and become impossible to resolve after weeks. AccountEX automatically reconciles every payout with bank transactions
- Track gateway commissions separately from shipping costs and marketplace fees. Use different accounts (6840 for gateways, 6841 for marketplaces, 4400 for shipping) for precise cost analysis
- Use AccountEX to centralise multi-channel accounting: automatic import from Shopify, Amazon and WooCommerce, gateway reconciliation, VAT management on discounts and returns, and an always up-to-date Swiss balance sheet — from checkout to balance sheet, error-free
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