Prep the pan. Line a 12-cup muffin tin with paper liners and lightly spray them. Preheat the oven to 350°F (175°C).
Mix dry ingredients. In a large bowl, whisk the gluten-free flour, baking powder, baking soda, salt, cinnamon, and nutmeg until evenly combined.
Whisk the wet ingredients. Add eggs, applesauce, maple syrup (or coconut sugar), oil, vanilla, and non-dairy milk.
Whisk until smooth and glossy.
Combine gently. Add the wet mixture to the dry ingredients. Stir with a spatula until just combined. Avoid overmixing to keep the crumb tender.
Fold in apples. Stir in the diced apples and any optional add-ins.
The batter will be thick—this is good.
Portion the batter. Divide evenly among the muffin cups, filling about 3/4 full. Sprinkle with the cinnamon-coconut sugar topping if using.
Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick inserted in the center comes out clean or with a few moist crumbs.
Cool. Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps them set and improves texture.