Preheat your oven to 375°F (190°C) and position the rack in the center. Line a standard 12-cup muffin tin with paper liners or grease generously with non-stick spray.
Beat the softened cream cheese, ¼ cup granulated sugar, egg yolk, and ½ tsp vanilla extract together with a hand mixer on medium speed for 1–2 minutes until completely smooth. Set aside at room temperature.
In a large bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon until evenly combined.
In a second large bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract until smooth and glossy.
Add the dry ingredients to the wet ingredients and fold together gently with a rubber spatula until just combined — stop as soon as no flour streaks remain. Do not overmix.
Fill each muffin cup halfway with pumpkin batter, add 1–1½ tablespoons of cream cheese filling in the center, then top with more batter until cups are about ¾ full. Cover the filling completely with batter.
Bake at 375°F (190°C) for 20–24 minutes, until the tops spring back when lightly pressed and a toothpick inserted into the pumpkin portion (not the filling) comes out clean or with a few moist crumbs.
Cool the muffins in the tin for 5 minutes, then transfer to a wire rack. Allow at least 10–15 minutes before eating so the cream cheese filling can set to a creamy texture.