Prep your pan and oven. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or grease lightly.
Whisk dry ingredients. In a large bowl, whisk flour, protein powder, baking powder, baking soda, cinnamon, nutmeg, and salt until combined.
Mix wet ingredients. In a separate bowl, whisk eggs, yogurt, milk, maple syrup, oil, and vanilla until smooth.
Combine gently. Pour wet ingredients into dry. Stir with a spatula until just combined.
The batter should be thick but scoopable.
Fold in apples (and add-ins). Stir in chopped apples and any nuts or raisins. Don’t overmix.
Fill the muffin cups. Divide the batter evenly among the 12 cups. Sprinkle with a little coarse sugar and cinnamon if you like.
Bake. Bake for 17–21 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
Cool. Let muffins cool in the pan for 5 minutes, then transfer to a rack to cool fully.
This helps them set and keeps the texture tender.