Preheat oven to 375 F and grease baking dish big enough to hold peppers with oil or butter.
Cut tops of bell peppers, as you would a jack-o’-lantern. Discard seeds and membranes. Remove stems from tops and discard, reserving tops for filling. Dice tops.
Place peppers cut side up in prepared dish. If peppers won’t stand up, you can slice some of their bottoms off to even them out.
In bowl, mix protein, grain, sauce, and any optional add-ins with diced pepper tops and season to taste with salt and pepper. Mix in cheese, reserving a little to use as garnish. Spoon stuffing into peppers and sprinkle cheese over top.
Pour just enough water in baking dish to cover the bottom. Cover peppers loosely with compostable parchment, silicone baking mat, or top of a pot or pan.
Bake for 20 minutes, then uncover and bake for an additional 5 to 10 minutes to brown the tops. The filling should be heated through and peppers softened.