Preheat your oven to 350°F (175°C) and line a cupcake pan with paper liners, ready for batter.
In a large mixing bowl, whisk together the flour, cinnamon, nutmeg, baking powder, and salt until well combined and fragrant.
In a separate bowl, beat the softened butter, granulated sugar, and brown sugar with a whisk or mixer until light and fluffy, about 2-3 minutes, and the mixture looks creamy and pale.
Add the eggs one at a time, beating well after each addition, until the batter is smooth and slightly thickened.
Mix in the pumpkin puree and vanilla extract until evenly incorporated. The batter may look slightly grainy but well combined.
Gradually fold the dry ingredients into the wet mixture using a spatula, just until combined and no streaks remain, being careful not to overmix.
Spoon the batter evenly into the paper liners, filling each about two-thirds full. The batter should look moist and slightly domed on top.
Bake in the preheated oven for 20-22 minutes, or until a toothpick inserted into the center comes out clean and the cupcakes are golden at the edges. The tops will feel springy to the touch.
Remove the cupcakes from the oven, and let them cool in the pan for 5 minutes before transferring to a wire rack. They should be moist and fragrant when cooled slightly.
While the cupcakes cool, beat the softened cream cheese and butter together until smooth and creamy, about 2 minutes.
Gradually add the powdered sugar, about a half cup at a time, beating well after each addition until the frosting is fluffy and spreadable. Mix in vanilla for flavor.
Once the cupcakes are completely cooled, pipe or spread the cream cheese frosting on top of each cupcake, creating a smooth or decorative swirl.
Enjoy your spiced pumpkin cupcakes immediately for the best flavor and texture, or store them in an airtight container until ready to serve.
