Preheat your oven to 350°F (175°C). Grease a muffin tin or line with paper liners.
In a large mixing bowl, whisk together the flour, sugar, baking powder, and salt.
In another bowl, mix the cooked quinoa, milk, vegetable oil, vanilla extract, and eggs until well combined.
Pour the wet ingredients into the dry ingredients and stir until just combined. Fold in the chopped pecans and dark chocolate chips.
Divide the batter evenly among the muffin cups.
Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.