Preheat oven to 350°F. Prepare a muffin tin with paper liners or by lightly greasing or buttering. Set aside.
In a medium sized bowl combine the flour, baking powder, baking soda, spices and salt. Stir to combine and set aside.
In a bowl with a handheld mixer or the bowl of your stand mixer beat the butter until soft and fluffy. Beat in the brown sugar until combined.
Add the eggs one at a time beating until combined. Add the vanilla and beat into the mixture.
Add the pumpkin and beat until combined again before adding the dry ingredients.
Mix until mostly combined before adding the chocolate chips and pepitas. Finish mixing just until everything is combined.
Divide batter evenly among the 12 cavities in the muffin tin. Sprinkle tops with extra chocolate chips and Pepita if desired. Place in the oven and bake 17-20 minutes until a toothpick inserted in the center comes out clean.
Remove muffins from the muffin tin and place on a cooling rack until cool. Once completely cool, muffins can be stored in an airtight bag or container for up to 5 days or frozen for up to 3 months.