Preheat oven to 350º Fahrenheit. Adjust oven racks as needed so muffin pan will sit in center of oven. Line cavities of muffin pan with cupcake liners. Set pan aside.
Crack eggs directly into large mixing bowl. Whisk eggs vigorously until well combined. Be careful not to overmix.
Add coconut sugar, coconut oil, and vanilla extract to bowl. Whisk or stir well until ingredients are fully combined.
Add drained pineapples, grated carrots, almond flour, coconut flour, tapioca flour, baking soda, salt, cinnamon, and ground ginger to bowl. Stir until all ingredients are fully incorporated, forming thick cupcake batter. Be careful not to over-stir or batter will become dense.
Once batter is prepared, add ½ cup chopped pecans. Gently fold pecans into batter to distribute.
Use cookie scoop or spatula to portion cupcake batter evenly into cupcake liners.
Place filled muffin pan in center of preheated oven. Bake cupcakes 20 minutes.
After 20 minutes, begin testing doneness by inserting toothpick into center of cupcakes, then immediately removing toothpick. Continue baking, checking doneness every 1 to 2 minutes, until toothpick can be removed cleanly, with few or no crumbs stuck to toothpick.
Once cupcakes are fully baked, carefully remove pan from oven and set aside. Let cupcakes rest in pan 5 minutes or until cool enough to handle, then transfer cupcakes from pan to wire cooling rack. Set cupcakes aside until completely cooled.