Preheat the oven to 375 degrees. Spray a 9x13 baking dish with nonstick spray.
Cook the rice according to the package instructions.
Cut peppers in half lengthwise, remove seeds, and place in the baking dish, cut side up.
Add the olive oil to a nonstick skillet over medium heat. Once the oil is hot, add the onion. Cook onions until tender, about 3-4 minutes, stirring occasionally.
Add the vegan meat to the nonstick skillet and cook until brown, about 8-10 minutes.
Add the minced garlic and cook for another minute, taking care not to burn the garlic.
Add the tomatoes, spices, salt, pepper and red pepper flakes. Reduce heat to medium low. Bring to a simmer and cook for about 3 minutes until the tomatoes are warmed.
Add the cooked rice and half of the cheese. Stir together. Cover with a lid and cook for 2-3 minutes until the cheese has melted. Remove the pan from the heat.
Divide the filling into the cut pepper halves and top with the remaining cheese.
Spray a sheet of aluminum foil and place it over the stuffed peppers, sprayed side down. This will keep the cheese from sticking to the foil.
Bake in a preheated oven for 30 minutes, then remove the foil and bake another 15 minutes or until the peppers are fork tender.