How do I mix warehouse stock and dropship on Shopify without losing track of margin?

Same storefront SKU. Two fulfillment modes. Two cost paths. Shopify will show one inventory number and one cost field. That is why margin disappears. This is not an intercompany dropship between two of your entities. That is a transfer price and an elimination. Here the vendor is outside the books, and the only cost that should exist is the PO that shipped.

Keep the two cost paths separate

Warehouse stock: you receive, WAC updates, you ship, COGS is the current blend (FOB plus landed freight and duty). Dropship: the customer order raises a supplier PO, the vendor ships, COGS is that PO (usually FOB, no warehouse receiving, no storage). Those units never touch your bin, so they must not average into warehouse WAC. Receiving a dropship confirm as if it were a warehouse receipt is how every later stock sale inherits a fake discount. A factory-direct channel should show a lower product cost than a DDP warehouse. That is expected. If you blend them, the warehouse average is wrong forever. Shopify's cost field is not WAC. Do not let a connector copy the vendor FOB into the warehouse SKU, or copy the warehouse blend onto the dropship invoice. 3PL storage on stock units is fulfillment, not a reason to pull dropship FOB into the warehouse average.

Route each line to one mode

Do not split one order line between own stock and dropship. Route the line to one mode. If the warehouse is short, the whole line dropships or the order waits. Available-to-sell for Shopify is warehouse ATS, not vendor fantasy stock, unless you truly sell the vendor's pile and you have a feed you trust. Hold a buffer on the warehouse publish. Do not publish dropship as if it were on-hand.

Recognize revenue on the shipment you own

Revenue waits for the shipment you actually own. Warehouse: recognize when you ship. Dropship: cash is not revenue until the vendor ships (and you have the confirm). Match the vendor invoice to that PO. That three-way does not touch the warehouse pile and must not move warehouse WAC. Contribution margin is the honest compare: price minus the cost path that shipped, minus outbound (your parcel or their freight), minus fees, minus returns. A dropship unit can look cheap on product cost and lose on their shipping and your refund rate. A dropship return is a vendor claim or a vendor credit, not a zero-cost receipt into your bin. Tag the channel or the fulfillment mode on the invoice so the class P&L can separate them. If finance cannot say, for a SKU-week, how many units shipped from stock versus the vendor, you do not have a mix. You have a Shopify catalog and a mystery COGS.