Preheat oven to 375 degrees F.
In a small bowl, mix flaxseed and water. Let it sit for about 10 minutes to form a flax "egg."
Mix pumpkin, almond milk, lemon juice, maple syrup and vanilla.
Stir in the flax mixture.
Add both flours, baking powder, baking soda, salt, pumpkin pie spice and chocolate chips. Mix thoroughly until all ingredients are combined.
Fill muffin pan cups about 2/3 full.
Bake at 375 degrees F for 25 minutes.
Let muffins cool for 10 minutes before removing from muffin pan.