How do I calculate true contribution margin by channel for Shopify vs Amazon vs wholesale?

Same formula on every channel. Different fees. One set of GL accounts, tagged by class. Not a second chart of accounts.

Contribution margin vs gross margin

Contribution margin per unit is selling price, minus weighted average cost, minus outbound shipping and fulfillment, minus payment and marketplace fees, minus a returns allowance, minus the variable ads that actually bought the order. Express it on net revenue, not gross. Gross margin stops at price minus WAC. That is why Shopify can look healthier than Amazon until you put fulfillment and referral fees in the same row. Wholesale often has no ads and a fat freight-out or chargeback line. Compare contribution, or you will kill the wrong channel.

The fee stack by channel

The fee stack is what changes. Shopify: payment processing, Shop Pay or PayPal, 3PL pick-pack, outbound parcel, a returns allowance, the ads that bought that order. Amazon: referral fee, FBA fulfillment or inbound, storage if you treat it as variable, advertising, a returns allowance. Wholesale: freight-out, EDI or chargebacks that are really a price cut, almost no payment fee, almost no ads. Do not drop FBA fees into COGS to "fix" Amazon. Do not hide 3PL pick-pack inside unit cost. Those are fulfillment. They belong on this line, not in WAC.

Using WAC as the unit cost

WAC is the unit cost: the blend after receipts, supplier-invoice variances, and landed freight and duty. Last received price is not that number. BOM cost is not that number. Opening a PO does not move it. A kit built at ship time expenses live component averages even if the kit SKU still shows a leftover $1. One expensive DDP container re-prices every unit you still hold, so this month's Amazon fee is not why last month's Shopify margin moved. Factory-direct FOB should show a lower COGS than a DDP warehouse. That is expected, not an error. If FBA inbound really costs more than the 3PL, you need cost-by-warehouse. You cannot fake it with a second COGS account named Amazon.

Track channels with classes

Use classes (or dimensions) on the same sales, COGS, freight-out, fee, and returns accounts. Duplicate GLs per channel (Sales-Shopify, Sales-Amazon, COGS-Shopify, COGS-Amazon) make the trial balance unreadable and still fail when a SKU switches nodes. Stamp the class on the shipment or invoice when it posts. Do not allocate rent, salaries, or brand marketing into this number. Those are below contribution. Negative "margin SKUs" are usually priced below the current blend, or the blend is garbage. Reconcile valuation to the GL by SKU before you argue about ads. Then run the class P&L and subtract the variable lines the P&L does not already show. Do not restate historical COGS to make last quarter's Amazon look better.