Begin by slicing your butternut squash in half, carefully. Use a vegetable peeler to peel the skin off. Use a spoon to scoop out the seeds and guts of the squash. Slice the squash into 1 inch cubes. Set aside.
To make the butternut squash sauce, bring a large saucepan with olive oil or vegan butter to medium heat. Once warm, add the onions and cook, stirring, until tender (about 2-3 minutes).
Add the butternut squash and cook for about 5 minutes or until it begins to lightly brown. Add water until the squash is completely covered. Bring the pot to a low simmer, cover, and cook for 20 minutes.
While the butternut squash cooks, prepare the pasta. Bring a medium saucepan with olive oil and water to a boil. Add the pasta and cook, as instructed on the packaging, until tender. Strain, reserving 2-4 tablespoon of the pasta water. Set aside.
Once the butternut squash has simmered for 20 minutes, uncover and strain. Transfer the squash back into the pot so that you can use a handheld immersion blender to blend the cheese sauce. If you don't have an immersion blender, you can add the squash into a regular blender along with the following ingredients. Add the almond milk or oat milk, nutritional yeast, salt, and pepper. Use a handheld immersion blender to blend until creamy and silky smooth. Pour the sauce over the cooked pasta and stir.
You can enjoy the butternut squash macaroni just like this or you can continue to the next step for baking.