Prep your pan and oven: Heat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease the cups lightly.
Dice the apples: Peel if you prefer a smoother texture, or leave the skin on for extra fiber. Cut into small, even cubes (about 1/4 inch) so they bake evenly.
Mix the dry ingredients: In a large bowl, whisk flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
Keep it airy; no clumps.
Whisk the wet ingredients: In a separate bowl, whisk eggs, brown sugar, and granulated sugar until glossy. Add yogurt, oil, vanilla, and lemon juice. Whisk until smooth.
Combine wet and dry: Pour the wet mixture into the dry.
Stir gently with a spatula just until you see a few flour streaks left. Don’t overmix.
Fold in apples: Add the diced apples and fold until evenly distributed. The batter will be thick and chunky—this is good.
Fill the muffin cups: Divide the batter evenly among the 12 cups, nearly to the top.
Sprinkle with coarse sugar or cinnamon-sugar if using.
Bake: Bake for 18–22 minutes, until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs (no wet batter).
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack. Cooling helps set the crumb and keeps the bottoms from getting soggy.
Serve: Enjoy warm or at room temperature. A pat of butter or a drizzle of honey is a nice touch.