Prepare the oven and muffin pan: Preheat the oven to 425°F. Line a standard 12-cup muffin pan with paper liners or lightly grease each cup.
Combine the dry ingredients: In a large mixing bowl, whisk together the flour, baking powder, baking soda, kosher salt, cinnamon, ginger, cloves, and nutmeg until evenly combined.
1¾ cups all-purpose flour, 1½ teaspoons baking powder, ½ teaspoon baking soda, 1 teaspoon kosher salt, 2 teaspoons ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground cloves, ¼ teaspoon ground nutmeg
Mix the wet ingredients: In a separate large bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, neutral oil, eggs, vanilla extract, and milk until smooth and well combined.
1 (15-ounce) can pumpkin puree , ¾ cup granulated sugar, ½ cup light brown sugar, ½ cup neutral oil, 2 large eggs, 2 teaspoons vanilla extract, ¼ cup whole milk
Make the muffin batter: Add the wet mixture to the dry ingredients. Using a rubber spatula, gently fold the ingredients together just until only a few small streaks of flour remain. Avoid overmixing.
Add the chocolate chips: Gently fold 1 1/4 cups of the chocolate chips into the batter, reserving the remaining 1/4 cup for topping.
1½ cups semi-sweet chocolate chips
Fill the muffin pan: Divide the batter evenly between the 12 prepared muffin cups, filling each almost to the top. Sprinkle the reserved chocolate chips over the batter.
Bake at high heat: Bake at 425°F for 5 minutes. Then, without opening the oven door, reduce the oven temperature to 350°F.
Lower heat and finish baking: Continue baking at 350°F for another 15-20 minutes, or until the muffins are tall and golden and a toothpick inserted into the center comes out with just a few moist crumbs.
Cool: Let the muffins rest in the pan for 5 minutes before carefully transferring them to a wire cooling rack.