Preheat oven to 350° F. Line 12 cup muffin pan with parchment paper liners.
Combine all dry ingredients (flour, sugar, 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. Add eggs and yogurt to well. Whisk eggs into yogurt incorporating as little of flour as possible.
Add applesauce and lemon juice to yogurt and eggs. Whisk to mix, slowly incorporating in the flour.
Mix only until everything is incorporated, some lumps may remain. Over mixing will result in tough muffins. Gently fold in apple pieces.
Scoop batter into paper liners, filling to the top or slightly heaping.
Bake for 25-30 minutes until a cake tester comes out clean and the muffins are lightly browned.