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Place the crushed tomatoes, diced tomatoes and their juices, tomato paste, onion, garlic, bay leaves, basil, brown sugar, balsamic vinegar, oregano, red pepper flakes, salt, and pepper in a slow cooker, and stir thoroughly. Remove 1 1/2 cups of the mixture and set aside.
Slice off the tops of the bell peppers, remove the seeds and scrape them with a spoon to hollow them out. Place the bell peppers cut-side up inside the marinara sauce.
In a medium bowl, mix the black beans, quinoa, zucchini, and the reserved 1 1/2 cups of marinara sauce. Divide the filling evenly among the prepared bell peppers.
Cover and cook on low for 6 hours.