In a large bowl combine dry ingredients: flour, cinnamon, nutmeg, baking powder, baking soda, and salt.
In a medium bowl combine butter, brown sugar, eggs, and milk.
Add wet ingredients and carrots into dry ingredients, stir just until combined.
Pour muffin batter into the prepare cupcake pan filling each well about ⅔ full.
Bake for about 20 minutes or until a cake tester inserted into the middle of a muffin comes out clean.
Notes
Flour: Muffins are denser than cake, so this recipe uses whole wheat flour instead of cake flour. If you don't regularly use whole wheat flour don't make a special purchase. You can use all-purpose flour if you have that.Sugar: Muffins are also not as sweet as cake, so only uses some brown sugar. If you want less sugar in your muffins you can use a brown sugar substitute. If you want to lower the sugar content you can use Splenda or Swerve brown sugar instead.Make ahead of time: As always I make muffins in batches of 12-24 and then freeze them in freezer bags, so they will last longer. When I am ready to eat one I just defrost the muffin in the microwave for about a minute. You can also take a muffin out ahead of time and let it naturally defrost, but I never remember to do that.