amazon seller vs ebay

Business model: fulfillment vs. flexibility

Amazon's dominant model is FBA (Fulfillment by Amazon), where you ship inventory to Amazon warehouses and they handle picking, packing, shipping, and returns. That convenience comes at the cost of storage fees, fulfillment fees, and less control over your inventory once it's in Amazon's system. eBay, by contrast, is largely seller-fulfilled — you ship your own orders (or use your own 3PL), which means more manual work but more control over cost and timing.

This structural difference is the biggest driver of accounting complexity. FBA generates automated fee deductions, reimbursements, and inventory adjustments that need to be reconciled monthly. eBay's seller-fulfilled model puts more of that cost (shipping labels, packaging) directly into your books as a line item you control, rather than a fee schedule set by the platform.

Third-party sellers aren't a niche on Amazon — they're the majority of the business. Third-party sellers account for more than half of the physical gross merchandise sold on Amazon, which is why Amazon's fee structure, policies, and reimbursement rules matter so much to anyone building a business there.

Fee structure and margin math

Both platforms charge referral/final value fees as a percentage of sale price, plus optional fulfillment fees if you use FBA or eBay's managed shipping. Amazon layers on FBA storage fees (standard and long-term), removal/disposal fees, and various surcharges depending on category and size tier. eBay's fee structure is comparatively simpler — a final value fee on the total sale amount, insertion fees in some categories, and optional store subscription tiers that reduce per-listing costs.

Don't treat any fee percentage as fixed when you're modeling margins — Amazon and eBay both revise fee schedules periodically, sometimes by category. Always verify against the current published fee schedule before building projections, rather than relying on last year's numbers.

Where this gets tricky in the books is inventory-related adjustments. Since 2025, Amazon reimburses lost or damaged FBA inventory based on your manufacturing/sourcing cost rather than retail price — and if you haven't submitted your actual per-unit cost, Amazon uses its own estimate instead. That means underreported costs quietly shrink your reimbursements. eBay has no equivalent inventory-custody exposure since you typically hold and ship the product yourself.

Sales tax and 1099-K reporting

Both platforms now collect and remit sales tax on your behalf in most states, thanks to marketplace facilitator laws — nearly every U.S. state with a sales tax now requires platforms like Amazon and eBay to collect and remit tax on third-party sales. That's a relief compared to the pre-2018 world, where sellers had to track economic nexus themselves. This entire framework traces back to a single Supreme Court case: South Dakota v. Wayfair let states require out-of-state sellers to collect tax based on sales/transaction thresholds, not just physical presence — the ruling that made marketplace facilitator laws possible in the first place.

Where sellers still need to pay attention is 1099-K reporting. The IRS threshold for third-party platform reporting has been phased in over several years rather than staying fixed at the old level, so the dollar figure that triggers a 1099-K from Amazon or eBay may differ year to year — check the current IRS guidance rather than assuming last year's threshold applies.

If you sell on both platforms, you'll likely receive two separate 1099-Ks reporting gross payment volume, which won't match your actual revenue after fees, refunds, and chargebacks. Reconciling gross 1099-K totals against your P&L is a recurring headache for multichannel sellers, and it's exactly the kind of gap that causes mismatched filings if it's done by hand.

Running both: what changes in your books

Most sellers who start on one platform eventually add the other — Amazon for volume and discoverability, eBay for margin control, auction-style demand, or categories (used goods, collectibles, oddball sizes) that don't fit Amazon's catalog rules well. The moment you're on both, your accounting needs to normalize two very different data feeds: Amazon's FBA settlement reports with fee codes and reimbursements, and eBay's seller payouts with their own fee and refund structure.

Manually reconciling both in spreadsheets works until it doesn't — usually right around the time you have a sales tax notice, a 1099-K mismatch, or an FBA reimbursement dispute to sort out. That's the gap that purpose-built ecommerce accounting software for every channel is meant to close: pulling Amazon and eBay data into one clean ledger so your P&L reflects actual revenue, not gross platform payouts.