Bring 2 cups water and quinoa to a boil in a saucepan. Reduce heat to medium-low, cover, and simmer until quinoa is tender, about 20 minutes.
Preheat oven to 350 degrees F (175 degrees C). Line a baking sheet with parchment paper.
Blend 1 cup warm water and flax seeds in a blender until seeds are broken down; let sit until flax mixture is thickened, about 10 minutes.
Mix 2 cup cooked quinoa, spelt flour, amaranth flour, almonds, baking powder, and salt together in a bowl.
Combine agave nectar, crystallized sugar cane juice, molasses, almond extract, and vanilla extract with flax mixture and blend on high speed until smooth. Mix flax mixture with flour mixture until dough is thoroughly mixed.
Spoon dough onto the prepared baking sheet.
Bake in the preheated oven until cookies are lightly browned around the edges, 12 to 15 minutes.