Preheat the oven. Set your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners. Lightly spray the liners to prevent sticking.
Mix the dry ingredients. In a large bowl, whisk almond flour, coconut flour, baking powder, salt, and sweetener until no lumps remain.
Whisk the wet ingredients. In a separate bowl, whisk eggs, almond milk, melted butter (or coconut oil), and vanilla. Make sure the butter isn’t hot so it doesn’t scramble the eggs.
Combine the batter. Pour the wet mixture into the dry ingredients.
Stir until just combined. The batter will be thicker than traditional muffin batter—this is normal.
Fold in chocolate chips. Reserve a few for the tops if you like. Stir gently to distribute them evenly without overmixing.
Fill the muffin cups. Divide the batter evenly among the liners, filling each about 3/4 full.
Top with reserved chips for a bakery look.
Bake. Place in the center of the oven and bake for 18–22 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
Cool properly. Let the muffins cool in the pan for 5–10 minutes, then transfer to a wire rack. Almond flour muffins firm up as they cool, so don’t skip this step.
Serve. Enjoy warm or at room temperature. If you like a melty chocolate top, warm a muffin in the microwave for 10–15 seconds.