Preheat oven to 350 degrees Fahrenheit. Line a 12-cup muffin pan with paper liners. Combine all dry ingredients (flour, protein powder, baking powder, baking soda, spices, salt) in a large bowl. Whisk to evenly distribute everything.
Make a well in the center of the flour mixture and add the eggs and yogurt to the well. Whisk the eggs into the yogurt, incorporating as little of flour as possible. Add the applesauce, maple syrup and lemon juice to yogurt and eggs. Whisk to mix, slowly incorporating in the flour.
Mix only until everything is incorporated — it's OK if some lumps may remain as over-mixing will result in tough muffins. Gently fold in the apple pieces.
Scoop the batter into paper liners, filling to the top or slightly heaping. Bake for 25 to 30 minutes, until a cake tester (or toothpick) comes out clean and the muffins are lightly browned.