Bring a large pot of lightly salted water to a boil. Cook pasta in the boiling water, stirring occasionally, until tender yet firm to the bite, about 12 minutes.
Meanwhile, heat oil in a saucepan over medium heat. Saute onion and garlic until softened and lightly browned, about 5 minutes. Stir in whole wheat flour until combined. Stir in soy milk, pumpkin puree, and Cheddar cheese.
Drain pasta and mix into the sauce. Cook until heated through, about 5 minutes.