Preheat oven to 350 degrees
Line muffin tin with parchment paper baking cups or spray with non-stick spray.
In a medium sized bowl, combine flour, flax, baking soda, baking powder, cinnamon, pumpkin spice, salt and mix until combined.
In a larger bowl combine eggs, milk, honey, melted butter, vanilla and pumpkin. Whisk until mixed together.
Slowly mix flour mixture into wet mixture until just combined.
Fold in chocolate chips.
Divide batter between 12 prepare muffin cups.
Bake in preheated oven for 14-16 minutes or until you insert a toothpick in the middle of muffin and it comes out clean.
Remove muffins from oven and let cool.
Store leftover muffins in air tight container for up to four days or freezer for a month.