Preheat the oven to 350°. Cut the tops from the squash. Use a spoon to remove the inside flesh. Dice the flesh into small pieces and set aside.
Place the squash into a baking dish and drizzle with 1 tablespoon of olive oil. Season with some of the salt and pepper. Bake until the squash is just tender, about 10 minutes.
Pour the remaining 2 tablespoons olive oil in to a skillet over medium-high heat. Add the diced squash, eggplant, onion and pepper to the pan. Season with salt and pepper. Cook until the veggies are tender and begin to turn brown, about 5 to 8 minutes.
Add the chorizo sausage to the veggies. Stir and cook until the chorizo is browned and crumbly, about 3 to 5 minutes.
Stir in the beans and cheese.
Spoon the filling into the cousa squash. If you have extra filling, just spoon it around the squash . . . it’s all good! Reduce the heat to 300°. Bake until the squash is completely tender, about 10 to 15 minutes.