Preheat oven to 325F and line a 12 cup muffin pan with liners.
In a large bowl, mix pumpkin puree, eggs, honey, brown sugar, coconut oil or butter, milk, and vanilla extract until well combined. Stir in baking powder, baking soda, pumpkin spice and salt. Slowly add the flour, stirring until thick batter forms. Add 1 cup of chocolate chunks and mix.
Scoop batter into the muffin pan. Top with remaining 1/4 cup chocolate chunks and pumpkin seeds. Bake for 25 minutes or until a toothpick inserted into the center comes out clean.