Using a spiralizer, turn the zucchini into spaghetti-like noodles or use a vegetable peeler to create long, thin zucchini ribbons, then set them aside.
In a large pot, melt the coconut oil over medium heat and sauté the onion and carrot for 5 minutes. Add the bell pepper and asparagus and sauté until all the veggies are tender, about 8 minutes more. Add the garlic and sauté until fragrant, about 1 minute. Add the zucchini noodles, tomatoes, salt, basil, oregano, and red pepper flakes, and sauté until the zucchini is tender, 5 to 8 minutes.
Remove the pot from the heat. Sprinkle the cheese over the top and adjust the seasoning, if needed. Serve warm. Store leftovers in an airtight container in the refrigerator for up to 3 days.
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