Start by preheating your oven to 350°F (175°C). Line a 24-cup muffin tin with paper liners. I like using double liners so you can peel off the foil if needed.
In a large bowl, whisk together pumpkin, brown sugar, granulated sugar, vegetable oil, eggs, vanilla, and half of the mini chocolate chips. Combine until smooth and creamy, but don’t overmix.
Add flour, baking soda, salt, cinnamon, ginger, cloves, and nutmeg to the pumpkin mixture. Stir gently until just combined, keeping the batter light and airy.
In a separate bowl, beat cream cheese, sugar, egg, milk, and vanilla until smooth. This makes the deliciously tangy swirl for the muffins.
Drop spoonfuls of cream cheese mixture into the pumpkin batter, gently folding a few times so it swirls but doesn’t completely mix in.
Use an ice cream scoop to fill muffin liners evenly. Sprinkle remaining chocolate chips on top for a pretty, melty finish.
Bake for 18–20 minutes or until a toothpick inserted comes out clean. Let muffins cool for 5–10 minutes in the pan, then transfer to a wire rack.