Preheat the oven to 375°F. Line a muffin tin with parchment muffin liners or use a silicone muffin pan.
Make the flax eggs. Combine 2 tbsp ground flaxseed with 5 tbsp water. Stir well and set aside for about 10 minutes to thicken.
Combine the dry ingredients. In a mixing bowl, whisk together the almond flour, tapioca flour, cinnamon, and baking soda, breaking up any lumps.
Combine the wet ingredients. Once the flax eggs have thickened, add them to the mashed pear or banana, lemon juice, and vanilla. Stir until well combined.
Make the batter. Pour the wet ingredients into the dry ingredients and stir until just combined. Fold in the grated apple.
Fill the muffin tin. Divide the batter evenly among the muffin cups.
Bake for about 20 minutes for small muffins or about 28 minutes for large muffins, or until a toothpick or cake tester inserted into the centre comes out clean.
Cool. Allow the muffins to cool for a few minutes in the pan before transferring them to a cooling rack.