Bring another pot of water to boil and cook the pasta according to the package instructions.
Meanwhile, in a small sauce pan, heat the oil over medium heat and add the garlic. Saute until fragrant, about 2 minutes. Whisk in the flour, then slowly whisk in two cups of milk, whisking constantly until combined. Add the pumpkin and nutritional yeast and stir until slightly thickened, about 3 minutes.
Strain the pasta and transfer it to a large mixing bowl. Pour the pumpkin sauce over the pasta and stir until fully coated. Stir in the spinach and remaining 1/2 cup of almond milk.
Transfer the pasta to a large baking dish and cover with shredded cheese. Bake for 25 - 30 minutes until the cheese is browned.