Prep: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease.
Mix dry ingredients: In a large bowl, whisk almond flour, protein powder, baking powder, baking soda, and salt until evenly combined.
Whisk wet ingredients: In a separate bowl, whisk eggs, yogurt, milk, maple syrup, oil, and vanilla until smooth.
Combine: Pour wet into dry.
Stir with a spatula until just combined. If using add-ins, fold them in now. The batter will be thick but scoopable.
Fill the tin: Divide batter evenly among the 12 cups, filling each about 3/4 full.
Bake: Bake for 16–20 minutes, until the tops are set and a toothpick comes out with a few moist crumbs.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a rack to cool completely.
They firm up as they cool.