Yes, you can still process draft orders while vacation mode is on. The app only removes the checkout buttons from your online store, so you can keep using draft orders as usual.
Vacation mode only blocks the online store
Vacation mode only disables the Add to Cart button on your online store theme. Orders can still come through via Apple Pay, Shop Pay, Google Pay, Shop app, PayPal Express, saved cart links, and other sales channels. The app hides the button via frontend injection on your theme — it cannot block checkout at the API level. If you need to fully prevent orders, also pause inventory or disable sales channels directly in Shopify. This is the biggest misunderstanding about vacation mode: it does not make it impossible to place orders, only harder for customers using the standard store flow.
Originally from our Help Center