Preheat your oven to 350°F. As it preheats, prepare a 12-count cupcake pan with paper cupcake liners.
Add flour, sugar, baking soda, baking powder, cinnamon, salt, and nutmeg to a large bowl. Whisk dry ingredients until combined.
1½ cups granulated sugar, 1 teaspoon baking soda, ½ teaspoon baking powder, 1 teaspoon cinnamon, ½ teaspoon salt, ¼ teaspoon nutmeg, 1⅔ cups all-purpose flour
Carefully crack eggs into the flour mixture. Add pumpkin puree, canola oil, and water. Using a hand mixer, mix on low speed, scraping down the sides of the bowl with a spatula as necessary, until completely mixed.
2 eggs, 1½ cups pumpkin puree, ½ cup canola oil, ¼ cup water
Fill each cupcake liner about ⅔ of the way with batter. Bake for 18-22 minutes, or until a toothpick inserted at the center of the cupcake comes out clean.
Once ready, transfer the cupcakes to a cooling rack and allow them to cool completely as you prepare the cream cheese frosting.