Heat oil in a pot over medium heat; cook and stir onion until slightly tender, about 3 minutes. Add pumpkin and garlic; continue cooking for 3 minutes. Add chicken stock and nutmeg; bring to a boil. Reduce heat to medium-low, cover, and simmer until pumpkin is tender, about 10 minutes more.
Bring a large pot of lightly salted water to a boil; add penne and cook, stirring occasionally, until tender yet firm to the bite, about 11 minutes. Drain and transfer to serving bowls.
Mix bacon and parsley into pumpkin mixture; cook, stirring frequently, until bacon is cooked, 2 to 5 minutes. Add cream and cook until heated through, about 2 minutes more. Spoon sauce over pasta and top with Parmesan cheese.