Pre-heat oven to 350F and bring a pot of lightly salted water to a boil.
Cut off the tops of your bell peppers (save the tops!) and remove the seeds inside the bell peppers. Set aside until the water has boiled.
Dice up the tops of the bell peppers, shallots, garlic, and mushrooms. (note I'm using shallots because that's what I personally had on hand. If you have a small onion, that works too!)
Once the water has boiled and you're done dicing everything, put the bell peppers in and let them boil for around 5 minutes, until they've soften. Leave them on a rack to dry once they're done.
While the bell peppers are boiling, grab your skillet and on medium-high heat, start browning your ground beef (season with salt and pepper).
Once the beef has browned, mix in the diced bell peppers, mushrooms, shallots, garlic, chili flakes, and the strained tomatoes. After 3-5 minutes, stir in your rice.
When everything is cooked, start stuffing your bell peppers. I layered some cheese in the middle of the bell peppers as well as on top before placing them in the oven to bake for 20 minutes.
After 20 minutes or once your cheese as melted and browned a little, they're ready to be served.