Preheat oven to 350 degrees F.
Cook quinoa according to package directions and let cool for about 5 minutes.
In medium bowl, combine quinoa, flours, sugar, baking powder, salt, and 2 tablespoons chia seeds.
In a smaller bowl, whisk together milk, egg, yogurt and vanilla extract.
Slowly add to quinoa mixture and stir until just combined.
Divide mixture evenly among greased muffin tins and bake for about 25 to 30 minutes, until a toothpick inserted in the center comes out clean. Allow to cool for about 5 minutes and enjoy!