Prep your pan and oven: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil.
Whisk dry ingredients: In a large bowl, whisk almond flour, coconut flour, protein powder, baking powder, baking soda, cinnamon, nutmeg, and salt until evenly combined.
Break up any clumps.
Mix wet ingredients: In a separate bowl, whisk eggs, Greek yogurt, almond milk, sweetener, oil, and vanilla until smooth.
Combine: Pour the wet ingredients into the dry. Stir with a spatula just until you get a smooth, thick batter. It should be scoopable, not runny.
Fold in carrots and add-ins: Gently fold in the grated carrots and any optional nuts, coconut, or raisins.
Do not overmix.
Portion the batter: Divide evenly into the muffin cups, filling each about 3/4 full. Tap the pan lightly to settle the batter.
Bake: Bake for 16–20 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs. Protein bakes can dry out fast, so start checking at 15 minutes.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a rack to cool completely.
This helps them set and stay tender.
Make the optional topping: Stir cream cheese, yogurt, powdered sweetener, vanilla, and a pinch of salt until smooth. Spread a thin layer on cooled muffins or pipe for a neat finish.
Serve: Enjoy plain or topped. They pair well with coffee or a post-workout shake.