Sauté the Aromatics
Heat 1 tablespoon of olive oil in a large Dutch oven over medium heat. Add the chopped onion and cook for about 5 minutes until it starts to soften. Stir occasionally. Add the Italian seasoning, kosher salt, crushed red pepper flakes, and minced garlic. Cook for another 30 seconds until the garlic is fragrant.
Cook the Filling
Add the lentils, quinoa, vegetable broth, fire-roasted tomatoes with their juices, and sun-dried tomatoes to the pot. Bring the mixture to a boil, then reduce the heat to low. Cover and simmer for 25-28 minutes until the lentils are tender. Stir halfway through and add more broth if needed.
Prepare the Peppers
Preheat your oven to 400°F (200°C). Lightly coat a 9x13-inch baking dish with nonstick spray. Slice the bell peppers in half lengthwise, remove the seeds and membranes. Arrange them cut side up in the baking dish.
Drizzle and Pre-Bake the Peppers
Drizzle the insides of the peppers with the remaining 1 tablespoon of olive oil and sprinkle lightly with salt. Pour a thin layer of water into the bottom of the pan. Bake the peppers uncovered for 20 minutes to soften.
Fill the Peppers
Stir the nutritional yeast into the cooked lentil and quinoa mixture. Carefully fill each pepper half with the cooked mixture. If using, top with non-dairy mozzarella cheese or cashew cream.
Bake and Garnish
Return the baking dish to the oven and bake for an additional 5-10 minutes until the peppers are tender and the filling is hot. Sprinkle with fresh basil or parsley before serving.