Cook quinoa according to package directions and let cool.
In a large skillet, heat olive oil over medium-high heat. Add onion and pancetta and cook until pancetta begins to brown. Add zucchini, spinach and thyme and cook until zucchini is slightly browned. Remove from heat and let cool.
In a bowl, toss the vegetable mixture with the cooled quinoa, half of the cheese, and season to taste.
Slice the tops off the bell peppers leaving stems attached and set aside.
Discard seeds and membranes.
Fill peppers with the quinoa mixture and place on a lightly oiled baking sheet. Bake on middle rack for 20 minutes. Arrange the pepper tops on the baking sheet and return to oven for 10 more minutes.
Remove from oven and sprinkle the stuffed peppers with the remaining cheese. Set oven to broil.
Broil peppers for 1 or 2 minutes with the tops still on the baking sheet, taking care not to burn the cheese.
Remove from oven and cool slightly. Place tops on the peppers and serve immediately.
