Spray a 9 x 13-inch baking dish with nonstick cooking spray.
In a large heavy skillet, heat the oil over medium heat. Add the onions and sauté them for 3 – 5 minutes, stirring occasionally, until they soften. (Note: If you are using meat, add that now too, and brown it with the onions.) Preheat the oven to 375 degrees.
Add the quinoa to the skillet, stirring to coat it, and then add the tomato sauce, beans, and chilies or salsa verde. Bring it to a low boil, reduce the heat, and simmer it for 5 minutes, then add the tomatoes. Simmer the mixture for 10 more minutes, stirring occasionally.
Remove the mixture from the heat, and spoon equal amounts into the center of each tortilla. Top it with a handful of cheese. Fold the tortillas burrito style (first fold in the ends, then roll it up), and lay them seam-side down in the baking dish. (At this point, you can bake them or refrigerate them for up to 12 hours.)
Bake the chimichangas for 15 - 20 minutes until they are lightly browned and heated through. Serve with a scoop of extra salsa, if desired.