E-Commerce Accounting: Handling Marketplace Sales, Refunds, and Fees
Small Business · 2026-01-20 · 7 min
Selling on Amazon, Shopify, and Etsy creates complex accounting: marketplace fees, shipping, refunds, and multi-state sales tax. Here is how to handle it cleanly.
E-commerce accounting is complicated because you do not receive the full sales price. When you sell a $50 item on Amazon, you might receive $37 after referral fees, FBA fees, and shipping costs. Your accounting needs to record the gross sale ($50), the fees ($13), and the net deposit ($37). Recording only the deposit understates revenue and misses deductible fees.
Refunds add another layer. A refund is not negative revenue — it is a separate transaction that reduces gross revenue. Some marketplaces refund the customer but charge you a restocking or processing fee, so you lose more than the original sale amount. Track refunds as their own line item so you can see your true return rate and its cost.
Sales tax for e-commerce is notoriously complex. In the US, you owe sales tax in states where you have nexus — which, after the Wayfair decision, includes any state where you exceed economic nexus thresholds (typically $100,000 in sales or 200 transactions). Most marketplaces now collect and remit sales tax on your behalf, but you still need to verify and report.
The cleanest approach: import marketplace settlement reports (not individual transactions) into your accounting system. Settlement reports show the net amounts deposited to your bank, broken down by sales, fees, refunds, and tax. Reconcile these against your bank deposits monthly. This is how professional e-commerce accountants handle high-volume sellers.
FiscalFlo — AI accounting that reads receipts, invoices, and bank statements automatically. Free tier: 15 documents a month.