Preheat oven to 350 degrees F (175 degrees C). Line a baking sheet with parchment paper.
Mix chia seeds and water together in a bowl; let sit until "chia egg" is thickened, about 10 minutes.
Stir spelt flour, amaranth flour, oat flour, baking soda, and salt together in a bowl. Blend "chia egg", almond milk, tahini, agave nectar, crystallized sugar cane juice, olive oil, and vanilla extract together in a blender until smooth; stir into flour mixture until dough is well mixed. Fold chocolate chips into dough; spoon onto the prepared baking sheet. Press dough onto baking sheet to flatten.
Bake in the preheated oven until edges of cookies are lightly browned, 10 to 15 minutes.