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Preheat the oven to 350°F.
Lighlty oil a 12-cup muffin tin or line with cupcake liners and set aside.
In a large bowl whisk together the flours, cinnamon, baking soda, baking powder, salt, and ginger until well combined then set aside.
In a separate large bowl whisk together the eggs, honey, oil, milk, yogurt, and vanilla until well combined.
Pour the bowl of dry ingredients into the bowl of wet ingredients and stir until well combined.
Now stir in the carrots and pecans until well combined.
Evenly divide the batter into the muffin cups filling them between ½ and ⅔ of the way full.
Bake in the preheated oven for about 20 minutes or until a toothpick inserted in the center comes out clean.
Take the cupcakes out of the oven and allow to cool for at least 30 minutes.
Mix the frosting ingredients (cream cheese, honey, yogurt, vanilla) together in a stand mixer or by hand in a large bowl until smooth.
When the cupcakes are completely cool spread the frosting on top of the cupcakes.