Preheat the oven to 350F. Combine the quinoa and water in a small saucepan and bring the water to a boil. Cover and reduce the heat, cooking until the quinoa is tender, about 15 minutes. Fluff with a fork and set aside.
Place the bell peppers cut-side down on a baking sheet and bake them for 10 minutes. Remove from the oven and set aside.
In the meantime, melt the coconut oil in a large pot over medium heat and saute the onion until it starts to become translucent, about 5 minutes. Add in the garlic, mushrooms and zucchini, and saute until all of the vegetables are tender, about 6 to 8 minutes. Season with salt and pepper.
Add in the cooked quiona, beans, and marinara sauce, and stir well to combine and adjust the seasoning to taste. Arrange the cooked bell peppers cut-side-up and spoon the filling into each pepper. It should generously fill 4 bell peppers. Spoon additional marinara sauce over each pepper to help prevent them from drying out, then bake for 30 minutes at 350, until the peppers are very tender. Serve warm, with additional marinara sauce, if you like.