Review all recipe notes and instructions before beginning.
Preheat the oven to 375 degrees. Line a nonstick 12 cup muffin pan with cupcake liners. (If not using liners, grease well instead.) In the bowl of a stand mixer fitted with the paddle/whisk attachment (or large bowl with a hand mixer), add the brown sugar, oil, eggs, and vanilla. Mix on medium low until combined.
On low mix in the carrot and mashed banana until just combined.
In this order add the flour, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg. Fold the dry ingredients in with a spatula until just combined.
In a separate bowl, using the stand mixer fitted with the paddle/whisk attachment or a hand mixer, beat the cream cheese, sugar, and vanilla on medium high until completely combined and smooth.
Spoon a heaping spoonful (about 1.5 Tablespoons) of batter into the muffin cups. Layer 1 Tablespoon of the cream cheese mixture on top of the batter. Fill the cups to the top with the remaining batter.
Bake for 20-22 minutes or until a toothpick comes out clean.