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Preheat the oven to 350°F. Line a muffin pan with cupcake liners.
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In a large bowl, sift together flour, cinnamon, ginger, all spice, baking powder, and baking soda. Set aside.
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In a medium bowl, beat butter and the sugar until fluffy. In scoops, add the pumpkin puree slowly and mix well. Add eggs one at a time, and then add vanilla. Blend for a minute on medium speed.
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Slowly add the dry ingredients and blend to ensure there are no clumps.
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Fill each cupcake liner about halfway full. Place the muffin tin on a baking sheet and bake until golden brown, 15-25 minutes.
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For the frosting, add the cream cheese, butter, salt and confectioners’ sugar in a large bowl and beat on medium speed until creamy.
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Once the cupcakes have cooled, add frosting and top with bacon bits.
