Preheat oven to 350ºF. Line muffin pan with 15 muffin liners.
In a medium bowl, whisk together all dry ingredients (1 3/4 cups all-purpose flour, 1 1/4 teaspoon baking powder, 1 teaspoon baking soda, 1/4 teaspoon salt, 1 1/2 teaspoons cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon nutmeg, 1/4 teaspoon ground cloves; set aside.
In a large bowl, stir together all wet ingredients (1 cup canned pure pumpkin puree , 1/3 cup vegetable or canola oil, 1 1/4 cup brown sugar, 2 large eggs, 1/3 cup milk). Add the dry mixture to the wet mixture. Do this gradually, incorporating until no flour streaks remain. Don't over-mix batter.
Spoon the batter evenly in the prepared muffin cups, filling each about 2/3 full (about 3 tablespoons of batter for each cupcake).
Bake for about 20 minutes and until a toothpick inserted into the center comes out clean. Let cupcakes cool for 10 minutes, then transfer to a wire cooling rack. Let cupcakes cool completely before adding the frosting.
For the cream cheese frosting
With an electric mixer, beat the 3/4 cup unsalted butter (at room temperature) until fluffy, about 2 minutes. Add the 8 ounces cream cheese (at room temperature), 1 1/2 teaspoons vanilla extract and 2 teaspoons cinnamon and continue to beat for another 2 minutes.
Turn the mixer down to a low speed and add in the 3 cups powdered sugar about 1 cup at a time. Mix until fully combined. Turn mixer back up to a higher speed and beat until fluffy, about 2 minutes.
Frost the cooled cupcakes using a flat knife or piping bag.
Cupcakes will keep well at room temperature for 4-6 hours. Refrigerate for up to 4 days.
Notes
Freeze: Cupcakes will keep well in the freezer for up to 3 months. I recommend tightly wrapping each cupcake individually in a freezer safe plastic wrap for best results. Thaw either in the fridge or at room temperature.
Make ahead: Cupcakes can be made the day before you plan to serve them. Store them in an airtight container at room temperature. Frosting can also be made the day before. Store frosting in an airtight container in the fridge. Allow frosting to come to room temperature before using.
Nutritional information: Keep in mind that the nutritional info is calculated with the entire frosting recipe. There is a good chance you will not use all of the frosting, particularly if you are frosting with a knife, and in that case calories and fat would be lower.
This cupcake recipe was originally published November 2019. It was updated and republished October 2023 and again October 2025.