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.
For the Cream Cheese Frosting
Add softened cream cheese, maple syrup, softened coconut oil, vanilla extract, and ginger to medium mixing bowl or stand mixer bowl.
Use hand mixer or stand mixer to whip ingredients together until ingredients are fully combined and mixture is smooth and fluffy.
Use offset spatula or butter knife to dollop frosting onto center of cupcake top, then smooth dollop out to cover top of cupcake completely. Repeat until all cupcakes have been frosted. Alternately, transfer frosting to piping bag fitted with piping tip of choice, then pipe frosting directly onto cupcakes in spiral motion.
If desired, garnish top of frosting with additional chopped pecans. Serve immediately, or arrange cupcakes on tray or platter until ready to serve.
Recipe Notes
Cupcake Liners: Parchment paper liners are so non-stick that they typically don't stay on these cupcakes well. If you're displaying these or just want them to have cute cupcake liners, I recommend using regular paper liners instead of parchment paper.
Coconut Oil: Unrefined coconut oil will have a stronger coconut scent and flavor. If your coconut oil is solid at room temperature, warm it just enough to melt it completely, but not so much that it's hot.
Pineapple: Use organic crushed pineapple in organic pineapple juice if possible. If not, be sure your pineapple doesn't contain any added sugar or sugar substitutes.
Pecans: You can omit the pecans entirely, or replace them in the batter with an equal amount of chopped walnuts or raisins.
Frosting: For a totally smooth, not-at-all-lumpy frosting, the coconut oil needs to be quite soft, if not melted completely. If you need to melt the oil, be sure to give it time to solidify again before trying to frost the cupcakes.
Cream Cheese: If you're paleo or dairy free, use a dairy-free cream cheese like Kite Hill, Miyoko's, or Violife. If you're not dairy free, though, you can use traditional full-fat cream cheese instead!
Leftovers: Leftover cupcakes can be refrigerated in an airtight container up to 5 days. Because this recipe uses a cream cheese frosting, it's not recommend to store the cupcakes at room temperature.