Preheat oven, with baking stone, to 425F.
In a food processor or blender, add florets and pulse until cauliflower resembles rice. Place in a large microwave safe bowl, cover with a towel, and cook for 8 minutes. Remove and allow to cool.
Place cauliflower into a dish towel and squeeze out water. Squeeze until no water drips out.
Place cauliflower in medium bowl again and top with almond flour, salt, red pepper flakes, habanero jack cheese, and egg. Mix until thoroughly combined.
Pour crust onto parchment paper and spread into a 9-inch round.
Transfer parchment paper onto baking stone and bake for 15 minutes or until golden and crisp on edges.
Remove baking stone from oven and top crust with pesto, mozzarella, onion, and cherry tomatoes. Sprinkle with salt, pepper and minced jalapeño for a spicier pie.
Transfer to oven once more and bake for an additional 10 minutes or until mozzarella is bubbly.