Preheat your oven to 350°F (175°C) and grease or line a muffin tin with paper liners.
In a mixing bowl, whisk together the flour, baking powder, baking soda, cinnamon, nutmeg, and salt.
In a separate bowl, combine the pumpkin puree, granulated sugar, brown sugar, vegetable oil, milk, and eggs. Mix until smooth.
Gradually add the dry ingredients to the wet mixture, stirring gently until just combined. Be careful not to overmix.
Fold in the chocolate chips with a rubber spatula.
Evenly distribute the batter into the prepared muffin tin, filling each cup about two-thirds full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.