Cook quinoa in a large pot of boiling salted water, stirring occasionally, until tender, 10–12 minutes. Drain well and return to pot. Cover and let steam 10 minutes. Pour off any condensed water, then let cool. Set aside ¼ cup cooked quinoa for topping muffins.
Preheat oven to 180c. Coat a standard 12-cup muffin pan with nonstick spray (do not use muffin liners). Whisk flour, baking powder, cinnamon, and remaining 1 tsp. salt in a medium bowl.
Mash bananas, honey, and brown sugar in another medium bowl, preferably with a potato masher, until sugar is dissolved and banana is completely mashed. Add egg and continue to mash until combined. Stir in oil and vanilla.
Stir banana mixture into dry ingredients just until combined. Stir in blueberries and 2 cups quinoa. Divide batter among muffin cups. Sprinkle lightly with raw sugar and reserved 1/4 cup quinoa.
Bake muffins until tops are firm, just beginning to brown, and a tester inserted into muffins comes out clean, 30–40 minutes. Let cool slightly before serving.