Make the Cupcakes
Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together flour, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves.
In a large bowl, whisk together pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla until smooth.
Gradually add dry ingredients to wet ingredients, mixing until just combined. Do not overmix.
Divide batter evenly among cupcake liners, filling about 2/3 full.
Bake for 18–22 minutes, or until a toothpick inserted into the center comes out clean.
Cool cupcakes in the pan for 5 minutes, then transfer to a wire rack to cool completely before frosting.
Make the Cream Cheese Frosting
In a large bowl, beat cream cheese and butter with an electric mixer until smooth and creamy (about 2 minutes).
Gradually add powdered sugar, 1 cup at a time, beating until fluffy.
Add vanilla and a pinch of salt, beating until combined.
Spread or pipe frosting onto cooled cupcakes.