Preheat the oven to 325F and line a muffin pan with parchment or silicone liners.
Cut 12 thin crosswise slices of jalapeño for the top of the muffins, and finely dice the remaining peppers.
In a large bowl, whisk together the almond flour, coconut flour, baking powder, salt, and garlic powder. Stir in 1 cup of the cheese and the chopped jalapeños.
Add the eggs, butter, and almond milk and stir to combine well. Divide the mixture among the muffins cups and top with the remaining cheese and a slice of jalapeno.
Bake about 33 Minutes, until the tops are set and just firm to the touch, and a tester inserted in the center comes out clean. Remove and let cool completely in the pan.