Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
In a medium bowl, whisk together flour, cocoa powder, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice.
In a large bowl, whisk together the eggs, brown sugar, and granulated sugar.
Add pumpkin puree, vegetable oil, vanilla, and milk. Whisk until smooth.
Gradually add the dry ingredients to the wet mixture. Stir just until combined. Do not overmix.
Fold in the chocolate chips, reserving a few for the muffin tops.
Divide the batter evenly between the muffin cups, filling each about ¾ full.
Sprinkle the remaining chocolate chips over the tops.
Bake for 18–23 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer the muffins to a wire rack.