Known Limitations
Here are some known limitations with Multiple Ship To:
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Promo codes aren't supported in the Multiple Ship To flow. If someone tries to enter one, they'll see an error. If they enter a promo code with a single ship-to order and then switch to Multiple Ship To, the site also returns an error and removes the promo code automatically.
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Multiple Ship To is limited to defining one shipping method per shipping address. Shoppers can't create multiple shipping methods for the same address. For example, a user can't order one set of items to ship Home using the Standard shipping methods and another set of items shipping Home using a One Day shipping method.
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Checkout can be slower if you're using shipping methods with real-time rates, especially with Multiple Ship To orders. You should run performance tests before going live with real-time rates.
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Customized Online Forms aren't supported.
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Minimum quantity is set as a shipping minimum and not as an order minimum. You must comply with minimum quantity limitations on each of the lines/shipments of your order. Multiple Ship To doesn't take into account more items on another line.
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Multiple Ship To isn't compatible with Scriptable Cart, Pickup In Store, or SuiteTax.