Preheat oven to 375 degrees F (190 degrees C). Line a muffin tin with paper liners.
Sift whole wheat flour, quinoa flour, baking powder, baking soda, and salt into a large bowl.
Combine bananas, strawberries, honey, oil, egg, and vanilla extract in a blender; blend until small chunks remain or mixture is completely smooth. Pour over whole wheat flour mixture; mix until batter is combined.
Spoon batter into the prepared muffin cups.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, 20 to 25 minutes. Transfer to a wire rack to cool.