Preheat oven to 350 degrees. Place cupcake liners in your cupcake pan.
In a large mixing bowl, add in the pumpkin puree, peanut butter, vegetable oil, egg, and honey. Whisk together until combined.
Add in the baking soda, baking powder, and whole wheat flour. Switch to a spatula and stir until incorporated. The batter will be really thick and perfect for scooping out.
Scoop the batter and fill the cupcakes almost to the top of the liner.
Place in the preheated oven and let bake for 25 - 27 minutes or until done. Stick a tooth pick in the center of the pupcakes and if it comes out clean or with moist crumbs, it's done.
Let cool completely.
Frosting
In a large mixing bowl, add in the cream cheese, pumpkin, peanut butter and honey. Beat unitl thoroughly incorporated.
Spread the frosting with a butter knife. I had a problem with the pumpkin puree getting caught in my tip while trying to pipe it.
Store in the fridge.
Notes
To store any peanut butter pumpkin pupcakes, store in an air tight container out of direct sunlight at room temperature or in the refrigerator for up to 3 days.