Heat oven to 350 degrees. Line two large baking sheets with parchment paper.
In a mixing bowl, whisk together the whole wheat pastry flour, almond flour, baking soda, baking powder, and salt.
Place coconut oil, brown sugar, and coconut sugar in another mixing bowl and beat the ingredients together until they produce a smooth mixture. Add the egg and vanilla extract and bea them into the sugar mixture.
Add half of the flour mixture to the wet ingredients and stir until combined. Add the remaining flour mixture and stir until a smooth dough forms. Stir in the oats and chocolate chips. Place the cookie dough in the refrigerator for 15-20 minutes.
Roll the dough into 16 balls. Evenly space the balls of cookie dough on the two prepared baking sheets. Bake for 9-12 minutes, or until the bottoms of the cookies are golden brown. Allow to cool before serving.