First, get your oven ready by preheating it to 350°F (175°C). Line a 24-cup muffin pan with paper liners. In a large bowl, whisk together the canned pumpkin, dark brown sugar, granulated sugar, vegetable oil, eggs, and vanilla extract. Stir in ½ cup of the mini chocolate chips until everything is well combined.
In the same bowl, add the all-purpose flour, baking soda, salt, cinnamon, ginger, cloves, and nutmeg. Whisk the dry ingredients into the wet mixture until they are just combined. Be careful not to overmix, as this can lead to tough muffins.
In a separate medium bowl, prepare the cream cheese layer. Combine the room temperature cream cheese, sugar, egg, milk, and vanilla extract. Whisk until the mixture is smooth and creamy, with no lumps remaining.
Gently add the cream cheese mixture to the bowl of pumpkin batter in large spoonfuls. Using a knife or a spatula, swirl the two batters together just a few times. You want to create distinct ribbons of cream cheese, not a fully incorporated mixture.
Use an ice cream scoop to divide the batter evenly among the 24 prepared muffin liners. The scoop helps keep the swirls intact. Sprinkle the remaining ½ cup of mini chocolate chips over the tops of the muffins. Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean.