In a separate bowl combine the flour, oats, flaxseed meal, pumpkin spice, cinnamon, baking soda, and sea salt. Mix together.
Add the dry ingredients to the wet in batches, folding into the cookie dough batter until just combined.
Fold in the chocolate chips. Cover with a tea towel and refrigerate for 20 to 30 minutes.
Scoop 2 tablespoons of the cookie dough batter onto the tray to form a cookie shape. Continue until you've used all the cookie dough.
Bake for 15 minutes, or until lightly golden brown along the edges and bottom of the cookies.
Let cool for 5 minutes, then transfer to a cooling rack to cool completely.