Preheat the oven to 350°F. Spray a loaf pan with cooking spray. Set aside.
Place softened butter and sugar into a large mixing bowl. Mix until butter mixture is pale yellow and light and fluffy. Use a rubber spatula to scrape the sides of the bowl once or twice while mixing.
Whisk in eggs, one at a time. Add the cream cheese and vanilla. Beat until mixed well. Add the carrots and apples. Mix together. The batter will be thick and a little chunky.
In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
With a rubber spatula, fold the dry ingredients into the wet ingredients. Combine until no streaks of flour remain. Fold in pecans, if adding these. You want to make sure there's no flour streaks but you also want to be careful not to overmix.
Pour batter into your prepared pan. Bake for 25 to 30 minutes, or until a toothpick/tester inserted in the center comes out clean. Remove from oven and let bread cool in the pan for 5 to 10 minutes. When the pan is warm to the touch, remove bread from pan and let your loaf cool completely. Slice and enjoy!