Preheat oven to 350 degrees.
In a medium pot, add rinsed dry lentils and 3 cups hot water. Simmer for 20 minutes. Drain and set aside to cool.
In a large skillet, heat olive oil. Add onions, garlic and a pinch of salt and cook for 3-4 minutes until beginning to soften, add mushrooms and continue to cook for another 5-7 minutes until soft. Remove the onion mushroom mix from the skillet and place in a bowl.
Using the same skillet add the ground beef, a pinch of salt and cook until browned. Stir in the red pepper flakes, diced tomatoes with juice and tomato paste. Mix together and cook for 5 minutes. Add the onion mushroom mixture and the cooked lentils. Season with salt and pepper, taste, and adjust seasonings.
Place bell peppers in a large baking dish. Scoop the filling into the bell peppers until full. Place in the oven and roast for 25 minutes. Remove the peppers from the oven and top with queso fresco and fresh cilantro.