Preheat the oven to 350°F and line a large baking sheet with parchment paper.
In a mixing bowl combine the quinoa, oats, pecans, and flax seeds; stir well. Heat the maple syrup and the coconut oil in a small microwave-safe bowl on high for 20 seconds. Stir in the vanilla extract and salt then pour the wet ingredients over the dry and toss to coat.
Spread the quinoa mixture in a thin layer over the prepared baking sheet. Bake for 20 minutes or until golden brown, stirring twice during the cook time. Add the unsweetened coconut flakes during the last 5-8 minutes of cook time and allow them to turn golden brown before removing the pan from the oven.
Cool completely on the baking sheet, as it cools the granola will harden and begin to clump together. When cooled break up any large pieces of granola into small clusters, stir in the chocolate chips and store for up to 2 weeks in the refrigerator.