Preheat oven to 375 degrees Fahrenheit (190 degrees Celsius). Line a 12-cup muffin pan with paper liners.
Make the filling: Beat softened cream cheese until smooth and fluffy, 2-3 minutes. Add sugar and beat until well combined. Mix in egg yolk and vanilla until smooth. Set aside.
Make the batter: In a large bowl, whisk together pumpkin puree, sugars, oil, eggs, and vanilla until smooth.
In a separate bowl, whisk together flour, baking powder, baking soda, salt, and all spices.
Pour wet ingredients into dry ingredients and fold gently until just combined. Don't overmix.
Layer the muffins: Place a spoonful of batter in each muffin cup. Add 1-2 teaspoons of cream cheese filling in the center. Top with more batter, filling cups about three-quarters full.
Bake for 20-25 minutes, rotating halfway through, until tops are golden and spring back when lightly touched.
Cool in pan for 10 minutes, then transfer to a wire rack. Store refrigerated for up to 5 days or freeze for up to 3 months.