Preheat and prep. Heat oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease with butter or coconut oil.
Combine dry ingredients. In a large bowl, whisk almond flour, cocoa powder, coconut flour, baking powder, baking soda, salt, and sweetener until evenly blended with no cocoa clumps.
Mix wet ingredients. In a separate bowl, whisk eggs, almond milk, melted butter (or oil), vanilla, and coffee if using. Make sure the butter isn’t hot so it doesn’t scramble the eggs.
Bring it together. Pour the wet mixture into the dry ingredients. Stir gently with a spatula just until combined.
The batter should be thick but scoopable.
Add chocolate chips. Fold in sugar-free chocolate chips, reserving a few for the tops.
Fill the muffin tin. Divide batter evenly among the 12 cups, filling about 3/4 full. Sprinkle the reserved chips on top.
Bake. Bake for 18–22 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs (not wet batter).
Cool. Let muffins cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. This helps them firm up and prevents crumbling.