Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease the cups.
In a medium bowl, whisk together the flour, cocoa powder, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.
In a separate large bowl, whisk the eggs, brown sugar, and granulated sugar until well combined.
Add the pumpkin puree, vegetable oil, vanilla extract, and milk. Whisk until smooth.
Gradually add the dry ingredients to the wet ingredients. Stir gently just until combined. Do not overmix.
Fold in the chocolate chips, reserving a few for topping.
Divide the batter evenly among 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 into the center comes out with a few moist crumbs.
Cool the muffins in the pan for 5 minutes, then transfer them to a wire rack.