Preheat oven to 350 degrees Fahrenheit. Coat a 12-muffin pan with non stick spray.
For the flax egg: In a small bowl combine the ground flax meal and water, let sit for 5 minutes.
In a medium sized bowl combine the gluten free flour, almond meal, baking soda, baking powder, and pumpkin pie spice. Whisk to combine and set aside.
In a large bowl combine the pumpkin, coconut oil, maple syrup, sugar, and vanilla. Add the flax egg and thoroughly mix until all ingredients are well incorporated.
Add dry ingredients to the wet and mix until well combined. Fold in the chocolate chips.
Evenly distribute the batter into greased muffin pan. Bake for 20-25 minutes, or until a tooth pick inserted into a muffin comes out clean.
Remove from oven and let cool in pan for 5 minutes before transferring to a cooling rack. Let cool completely and store in airtight container lined with parchment paper for 3-4 days.