Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, nutmeg, and salt until thoroughly combined and set aside.
In a large mixing bowl, use an electric mixer on medium speed to cream the softened butter, granulated sugar, and brown sugar together for 2-3 minutes, until the mixture becomes light and fluffy.
Beat the eggs into the butter-sugar mixture one at a time, ensuring each is fully incorporated before adding the next, then mix in the vanilla extract and pumpkin puree until the batter is smooth.
Gradually add the dry flour mixture to the wet ingredients in three parts, alternating with the milk in two parts, mixing on low speed after each addition just until combined, then gently fold in the chocolate chips with a spatula.
Divide the batter evenly among the prepared muffin cups, filling each about 3/4 full, and bake for 20-25 minutes, or until a toothpick inserted into the center of a cupcake comes out clean.
Allow the cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.