Preheat oven 400. Spray a 12 hole muffin tin liberally with cooking spray. Make sure to spray all the way up the sides and the top of the pan.
Combine the sausage with the almond flour, coconut flour, and ground flax. Divide into 12 pieces and press each piece into the bottom and up the sides of each muffin tin hole. Crack an egg into each. Sprinkle with the salt and pepper. Bake for 30 minutes.
Remove the tin from the oven and sprinkle the cheese and rosemary on top. Bake for an additional 5-10 minutes until the sausage is fully cooked (I stuck a meat thermometer into the crust to make sure it was 160) and the cheese is melted and bubbly.