Preheat the oven to 325°F (165°C). Lightly grease a 12-cup muffin pan and dust with flour.
In a large bowl, whisk together the all-purpose flour, almond flour, quinoa, baking powder, cinnamon, ginger, baking soda, and salt.
In another bowl, whisk the eggs, yogurt, milk, and honey until smooth.
Gently fold the wet mixture into the dry ingredients until just combined.
Carefully stir in the raspberries without overmixing.
Divide the batter evenly among the muffin cups.
Bake the Berry Quinoa Muffins for 15–20 minutes, or until a toothpick inserted in the center comes out clean.
Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.