Position oven rack in middle of oven and preheat oven to 350 degrees F. Line muffin tin(s) with cupcake liners. This batch makes 12 full muffins as shown in photos or 15 muffins level with the liners.
In a medium bowl, combine pumpkin puree, coconut oil, brown sugar, eggs and vanilla extract. In the same bowl, sprinkle the flours, pumpkin pie spice, cinnamon, and chia seeds if using over the wet ingredients, and then sprinkle the baking soda and baking powder evenly over everything. Stir until well incorporated and the flours are well mixed in (Note: whole wheat flour can be stirred much more than all-purpose flour without creating a tough finished texture and since the almond flour is gluten-free, it can be stirred in even more with successful results).
Now add your chocolate chips and give the mixture one last good stir.
Fill muffin cups between 1/2 to 3/4 full, depending on the size muffins you want. I filled mine 3/4 full. They don't rise a lot, so if you want really big muffins, fill even more. Sprinkle with more chia seeds if you like.
Bake for 22-25 minutes, until a toothpick inserted in the center comes out clean and tops begin to dry at the peaks. Place tin on cooling rack and cool completely.
For even better muffins, remove from tins when cooled and place in air-tight container for 24 hours before serving.