Preheat oven to 350ºF. Line an 8x8-inch baking pan with parchment paper and set aside. Whisk together the flaxseed and water and set aside. Allow to gel for 3-4 minutes.
Beat together the applesauce and peanut butter until creamy. Add the sugar and flax mixture. Beat until combined. Add the quinoa flour, oats, baking soda, and salt and mix until incorporated. Fold in the chocolate chunks (or chips).
Transfer the batter to the prepared baking pan. Press it into the corners of the pan using wet hands or a pastry roller. Bake on the center oven rack for 20-24 minutes.
Let the bars cool in the pan completely before slicing. (Bars can be stored in an airtight container at room temperature for up to 2 days. Freeze for longer storage.)