Preheat the oven to 375°F and line a muffin tin with liners.
In a large bowl, mash the bananas, then add coconut sugar, vanilla extract, coconut oil, and almond butter. Whisk until combined, then mix in shredded carrots.
Add gluten-free flour, cinnamon, nutmeg, salt, and baking soda. Use a spatula to combine well.
Use a double cookie scoop to divide batter into muffin liners. Gently press down on each muffin.
In a bowl or stand mixer, whisk softened cream cheese, milk, gluten-free flour, vanilla, and cream cheese until creamy.
Transfer frosting to a piping bag or plastic bag with a corner cut off. Insert into each muffin and squeeze until frosting comes out on top.
Bake for 23 minutes, then let cool for 30 minutes before serving.