Preheat the oven to 350°F. Grease a standard 12-cup muffin tin or line it with paper liners.
If your quinoa was just cooked, spread it out and let it cool for about 5 minutes so it is no longer steaming.
In a medium bowl combine 2 cups cooked quinoa, 1 cup whole wheat flour, 1 cup all-purpose flour, 1 1/2 tsp baking powder, 1 tsp salt, and 2 Tbsp chia seeds. Stir until the dry ingredients are evenly distributed.
In a separate bowl whisk together 3/4 cup unsweetened almond milk, 1 egg, 1/4 cup plain Greek yogurt, 1/3 cup honey, and 1 tsp vanilla extract until smooth.
Pour the wet mixture into the bowl with the dry mixture and gently fold with a spatula until just combined. Do not overmix—the batter will be thick and slightly lumpy.
Divide the batter evenly among the prepared muffin cups, filling each about three-quarters full.
Bake for 25 to 30 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Let the muffins cool in the tin for about 5 minutes, then transfer them to a wire rack or plate to cool slightly before serving.