Preheat your oven to 350°F (175°C). Grease a 12-cup muffin tin with cooking spray or line with muffin liners.
In a large mixing bowl, whisk together the self-rising flour, cinnamon, and nutmeg (if using).
In another bowl, combine the applesauce, Greek yogurt, egg whites, vanilla extract, and almond milk.
Gradually mix the wet ingredients into the dry ingredients, stirring until just combined. Be careful not to overmix.
Evenly distribute the batter into the muffin cups, filling each about ⅔ of the way full.
If desired, mix the cinnamon and sugar substitute for the topping. Lightly sprinkle the mixture on top of each muffin before baking.
Place the muffin tin in the preheated oven and bake for 15-18 minutes, or until a toothpick inserted in the center comes out clean.
Let the muffins cool for a few minutes in the tin before transferring them to a wire rack to cool completely.
