Preheat oven to 350℉. Line muffin tins with paper liners or spray with grease.
In a large mixing bowl, whisk together the flour, flax seed, baking soda, cinnamon, pumpkin pie spice, and salt. Set aside while mixing wet ingredients.
In another large mixing bowl, whisk together the pumpkin puree, oil, greek yogurt, eggs, sugars, and vanilla extract. Mix until well combined.
Gradually add the dry ingredients to the wet ingredients about 1/2 cup at a time and mix until combined.
Spoon batter into muffin tins, filling each cup to about 2/3 full.
Bake for 20-25 minutes, or until a toothpick or knife inserted comes out clean. (It's usually 25 minutes for me)
Allow muffins to cool for about 5 minutes in muffin tin before transferring them to a wire rack to cool completely.
Serve warm with butter!