Preheat oven to 350 degrees. Line a muffin pan with liners and set aside.
Whisk dry ingredients (flour through cinnamon) in a large bowl.
Mix wet ingredients (bananas through carrots) in a separate, small bowl.
Make a well in the flour mixture and add wet ingredients. Stir with a spatula until just combined (be sure not to over-mix).
Fold in crystallized ginger. Evenly distribute the batter between the 12 muffin liners.
Bake for 18-20 minutes or until a toothpick inserted in the center comes out clean. Cool for a few minutes in the pan, then transfer to a wire rack.
When cupcakes are completely cooled, make frosting: Add cream cheese, powdered sugar, and vanilla to a stand mixer (can also use a hand mixer) and beat on medium high until smooth. Frost cupcakes.