Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease the cups.
In a large bowl, whisk together the gluten free all-purpose flour, baking powder, baking soda, salt, and ground cinnamon.
In a separate medium bowl, beat the granulated sugar, brown sugar, and eggs until combined.
Add the unsweetened applesauce, Greek yogurt, vegetable oil, and vanilla extract to the sugar and egg mixture. Stir until smooth.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined.
Fold in the diced apples carefully, ensuring they are evenly distributed but do not overmix the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 22 to 25 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, then transfer to a wire rack to cool completely.