Preheat oven to 375 degrees. Line your cupcake tins with paper liners.
Add flour, cinnamon, nutmeg, ginger, clove, allspice, salt, baking powder, and baking soda; whisking all ingredients together.
In a second bowl, combine the butter and both sugars using your electric mixer until the mixture becomes light and creamy.
Slowly begin to add one egg at a time, beating to mix each egg as it is added to the butter and sugar mixture.
After the eggs have been added, add the milk and pumpkin puree to the wet ingredients, stir to blend.
Begin adding the dry ingredients to the wet ingredients one tablespoon at a time until all of the dry ingredients have been blended into the wet ingredients.
Using an ice cream scoop transfer the cupcake batter into the lined cupcake tins until each cup is ½ filled.
Bake at 350 degrees for 10 minutes and remove from oven.
Use a pastry bag with a large tip to pipe the pumpkin filling into the center of each cupcake.
Put the cupcakes back into the oven and continue to bake for an additional 15 minutes.
When the cupcakes are done take out of the oven and allow to cool slightly before transferring them to a wire rack to cool completely.
Making the frosting/ frosting the cupcakes:
Add the cream cheese and butter together in a mixing bowl.
Using your electric mixer beat the butter and cream cheese together until they are soft.
Slowly add tablespoons of the powdered sugar in the bowl beating after each addition.
Lastly, blend in the vanilla, mixing until completely blended.
Spoon the frosting into a pastry bag with a #13 tip.
Squeeze the open end of the pastry bag pushing the frosting to the tip.
Begin frosting from the outside edge of the cupcake in a circular motion working towards the center of the cupcake.