Preheat your oven to 350°F (175°C).
Grease a muffin tin or line it with muffin liners.
In a large mixing bowl, combine the whole wheat flour, all-purpose flour, baking powder, salt, and chia seeds. Whisk until well mixed.
In another bowl, whisk together the cooked quinoa, Greek yogurt, almond milk, egg, honey, and vanilla extract until well incorporated.
Pour the wet mixture into the bowl of dry ingredients. Gently fold them together until just combined.
Scoop the batter into the prepared muffin tin, filling each cup about two-thirds full.
Bake for 18-20 minutes, or until a toothpick inserted comes out clean.
Remove muffins from the oven and let them cool in the tin for 5 minutes before transferring to a cooling rack.
