In a small bowl, whisk the quinoa, flour, baking soda, cinnamon, and salt. Set aside.
Using a hand mixer or a stand mixer fitted with the paddle attachment, cream the butter with the brown sugar. Add the honey, mashed banana, applesauce, and vanilla extract and mix until combined. Fold the dry ingredients into the wet ingredients. Stir in the raisins.
Cover and chill the dough in the refrigerator for at least 1 hour.
Preheat oven to 350°F and line a baking sheet with parchment paper. Scoop the dough into balls and place on the baking sheet, about 2 inches apart. Bake for 18-20 minutes. The cookies may still seem soft and not done, but remove from oven and allow them to cool for 10 minutes.
Notes
While I have not tested it yet myself, if you're having trouble finding the quinoa flakes, you should be able to swap in rolled oats as a 1:1 substitute.