Fill a medium saucepan with water and bring it to a boil over high heat. Add the quinoa, reduce the heat to low, and simmer until the grains have popped open and appear translucent, about 12 minutes. Drain the grains in a fine mesh sieve and rinse them with cool water.
Position the rack in the center of the oven and heat to 400°. Use a crumpled sheet of waxed paper to lightly butter the wells of a muffin tin.
In a medium bowl, whisk together both flours, and the baking powder, cinnamon, and salt until well blended.
In a large bowl, with a hand mixer set at medium speed, beat together the brown sugar, peanut butter, and butter, scraping down the sides as needed, until smooth and creamy, about 5 minutes. Beat in the egg yolk and vanilla until smooth, then beat in the quinoa, continuing to scrape down the sides as you work. Reduce the mixer's speed to low and gradually beat in the milk.
With a rubber spatula, fold the flour mixture into the wet ingredients. Next, fold in the cranberries and chocolate chips until they're evenly distributed in the batter.
In a large bowl with a mixer set at high speed and beaters that have been cleaned and dried (to ensure that the eggs whip), beat the egg whites until soft peaks form, about 1 minute. Use a rubber spatula to gently fold the egg whites into the batter.
With a large spoon or ice cream scoop, fill each well of the muffin tin three-quarters full with batter.
Bake the muffins until they're brown and firm, about 20 minutes, turning the pan halfway through. Cool them in the pan for 5 minutes, then transfer them to a rack to cool completely.
Quinoa is popularly referred to and prepared as a cereal grain, but it belongs to the same plant family as beets, chard, and spinach.
Cooled muffins can be sealed in ziplock bags and frozen up to four months. To defrost, let them sit at room temperature overnight, bake them at 300° for 20 minutes, or microwave them for 60 seconds.