Begin by preheating your oven to 350°F (175°C). Prepare a 12-cup muffin pan by lining it with paper liners or lightly greasing it with cooking spray or oil.
In a large mixing bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, baking soda, ground cinnamon, ground nutmeg, ground ginger, and salt until evenly combined.
In a separate bowl, mix together the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract. Stir well with a whisk or electric mixer until the mixture is smooth and free of lumps.
Gradually add the dry flour mixture into the wet pumpkin mixture, stirring gently until just combined. It’s important not to overmix; leaving a few lumps will ensure the muffins remain tender.
In a small bowl, use a hand mixer or a fork to beat the softened cream cheese, powdered sugar, and milk until the mixture is creamy and smooth. This will be your filling.
Spoon approximately 2/3 of the pumpkin batter into each muffin cup, filling them about three-quarters full. Then, carefully add a tablespoon of the cream cheese mixture into the center of each muffin, pressing it down slightly so it’s nestled into the batter. Finish by adding a small dollop of pumpkin batter on top, covering the cream cheese entirely.
Place the muffin pan into the preheated oven and bake for 20-25 minutes. Check for doneness by inserting a toothpick into the muffin (avoid the cream cheese). It should come out clean when the muffins are ready.
Once baked, allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack to cool completely.
Notes
For an inviting look, lightly dust the cooled muffins with powdered sugar and arrange them on a rustic wooden board.