Preheat and prep: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Mix dry ingredients: In a large bowl, whisk almond flour, coconut flour, protein powder, cocoa powder, baking powder, baking soda, and salt until evenly combined and lump-free.
Mix wet ingredients: In a separate bowl, whisk eggs, Greek yogurt, almond milk, sweetener, oil, vanilla, and coffee (if using) until smooth.
Combine: Pour the wet mixture into the dry ingredients. Stir with a spatula until just combined.
If the batter seems dry or very thick, add 1–2 tablespoons of almond milk. The batter should be thick but scoopable.
Add chips: Fold in chocolate chips, reserving a few to sprinkle on top if you like.
Fill the tin: Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle on any remaining chips.
Bake: Bake for 16–20 minutes, until the tops are set and a toothpick inserted into the center comes out mostly clean with a few moist crumbs.
Cool: Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This helps them firm up and improves texture.