Prepare the pasta by bringing a large pot of salted water to a boil. Cook according to package instructions until al dente. Before draining, reserve 2-3 tablespoons of the starchy pasta water.
Heat olive oil in a large skillet over medium heat. Add the diced onion and cook for 3-4 minutes until translucent, stirring occasionally.
Add minced garlic and sage to the skillet and cook for 30-60 seconds until fragrant, being careful not to burn the garlic.
Stir in the pumpkin puree and plant milk, whisking to combine until smooth. Let the sauce simmer gently for 2-3 minutes to thicken slightly.
Mix in the nutritional yeast, nutmeg, red pepper flakes (if using), and season with salt and black pepper to taste. Continue to simmer on low heat for 2 minutes.
Add the diced apple to the sauce and stir to combine. Cook for just 1-2 minutes—you want the apple to soften slightly but maintain some texture and bite.
Toss the drained pasta directly into the sauce, adding a splash of the reserved pasta water to help the sauce coat the pasta evenly. Stir gently to combine all ingredients.
Adjust the consistency if needed by adding more pasta water a tablespoon at a time until you reach your desired creaminess.
Serve immediately in warmed bowls, garnished with additional fresh sage leaves and toasted pumpkin seeds or walnuts if desired.