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Preheat your oven to 350 degrees. Line 2 muffin tins with cupcake liners.
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In a medium sized bowl, combine flour, spices, baking soda, and salt. Set aside.
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In the bowl of your mixer, cream oil, pumpkin puree, and sugars for 4 minutes on medium high speed.
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Add eggs, one at a time, incorporating fully before adding the 2nd egg.
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Add vanilla and mix until combined.
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Stir in flour mixture to the egg/pumpkin mixture.
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Fill muffin cups ⅔ of the way full. Set aside.
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In a separate bowl, whisk together softened cream cheese, egg yolk, and vanilla extract until smooth.
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Spoon a teaspoon of the cream cheese mixture onto each pumpkin muffin batter.
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Swirl with a toothpick or knife.
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Mix together cinnamon and sugar then sprinkle onto each muffin.
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Bake muffins for 18-20 minutes or until a knife is inserted and comes out clean.
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Cool in pan for 5 minutes then transfer muffins to a baking rack to cool completely.
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Store in an airtight container for up to 3 days, or freeze in a single layer in an airtight container or bag for up to 3 months.