Bring a large pot of salted water to boil. Preheat oven to 400°F.
Using a small spoon, hollow out the center of the zucchini halves, leaving 1/4-inch thick shell on each half. Chop the scooped out zucchini flesh and set aside 1 cup to use in the filling. Drop zucchini halves in boiling water and cook 1 minute. Remove from water and set aside.
In a large skillet, heat the olive oil over medium-high heat. Add the onion and cook until translucent, about 4-5 minutes.
Squeeze the 1 cup of zucchini filling in a paper towel to remove excess moisture. Stir in the zucchini, garlic, red pepper, corn, chili powder, cumin, lime juice, and cilantro. Cook for 2-3 minutes. Remove from heat and stir in the black beans and quinoa. Season with salt and black pepper, to taste. Stir in 1/2 cup of the shredded cheese and 1/2 cup of the enchilada sauce.
Spray two 9x13 baking dishes with nonstick cooking spray. Drizzle a little bit of the enchilada sauce at the bottom of each pan. Place the hollowed out zucchini cut side up in the dish. Using a spoon, fill the zucchini equally with the black bean and quinoa filling, pressing firmly so it stays in the zucchini. Drizzle the remaining enchilada sauce over the filled zucchini. Sprinkle the remaining cheese evenly over the top.
Cover with foil and bake for 30 minutes. Remove the foil and bake for 5 more minutes or until cheese is melted and zucchini is cooked through. Serve warm.
Note-you can halve this recipe. This recipe reheats and freezes well.