Preheat your oven to 350°F (175°C) and line a 12-cup muffin pan with paper liners or grease lightly.
In a large bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt.
In a separate bowl, combine the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract. Mix until smooth and well combined.
Gradually incorporate the dry ingredients into the wet ingredients, stirring gently until just combined. Be careful not to overmix; a few lumps are okay.
In another small bowl, beat together the softened cream cheese, powdered sugar, and milk until smooth.
Fill each muffin cup with about 2/3 of the pumpkin muffin batter. Then, add a tablespoon of the cream cheese mixture into the center of each muffin, pressing it down slightly. Top with a little more pumpkin batter until just covered.
Bake in the preheated oven for 20-25 minutes or until a toothpick inserted into the muffins comes out clean (avoiding the cream cheese).
Allow to cool in the pan for about 5 minutes, then transfer to a wire rack to cool completely.
Notes
Dust the cooled muffins with a light sprinkle of powdered sugar and serve on a rustic wooden board or stand with a few cinnamon sticks for an autumn vibe.