Yes, Scotch Bonnet peppers can be frozen and used over a prolonged period of time. This is a great way to preserve their heat and flavor. Just wash the peppers, remove their stems, and place them in a single layer on a baking sheet inside the freezer. Once frozen, transfer them into an airtight container or freezer bag and store in the freezer. Scotch Bonnet peppers can be kept for up to six months when frozen.