Preheat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease the cups lightly.
In a large bowl, whisk together the gluten free flour, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger until well combined.
In a separate medium bowl, whisk the granulated sugar, brown sugar, and eggs until smooth and slightly fluffy.
Add the applesauce, apple cider, vegetable oil, and vanilla extract to the egg mixture. Whisk until fully combined.
Pour the wet ingredients into the dry ingredients and gently fold together with a spatula until just combined. Do not overmix.
Fold in the diced apple pieces evenly into the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the tin for 5 minutes.
Transfer the muffins to a wire rack to cool completely before serving.