Preheat the oven to 375ºF. Line a 12 pan muffin tin with paper liners or grease with coconut oil.
In a large bowl or mixer, combine the pumpkin, eggs, coconut oil, coconut sugar, vanilla extract and nut butter until fully combined.
Add the coconut flour, cinnamon, nutmeg, baking soda, baking powder, and sea salt to the wet ingredients and mix well.
Divide the batter between the prepared muffin tins. In a small bowl, stir together the coconut sugar, cinnamon, and pepitas and sprinkle on top of the muffins.
Bake in the preheated oven for 20-25 or until a toothpick inserted into the center of a muffin comes out clean.
Remove from oven and allow to cool on a wire rack for about 10 minutes. Flip out onto a cooling rack to finish cooling.
Store sealed in the refrigerator. They also freeze well!