Add onions, coriander, cumin and pepper flakes, and cook, stirring occasionally, until the onions soften and the spices smell toasted, about 6 minutes.
Add the ground meat and 1/2 teaspoon of salt and cook, breaking it up into clusters with a spoon, until done.
Reduce heat to low and add quinoa and 1-1/2 cups water. Cover and simmer until quinoa plumps and most of the liquid is absorbed, about 25 minutes.
Meanwhile, preheat the oven to 375 F.
Cut off the tops of the peppers and use a teaspoon to remove the seeds and ribs. Take a very thin slice off the bottom of each pepper to stabilize them and arrange them in a 13 x 9-inch baking dish.