Preheat the oven to 375℉ and grease a 9x13 baking dish.
Cook the elbow macaroni in salted boiling water for 2 minutes less than the recommended time. Drain and set aside.
Melt the butter in a saucepan over medium heat. Whisk in the flour and cook for 1 to 2 minutes until smooth.
Slowly pour in the milk while whisking to prevent lumps. Continue cooking until the sauce thickens and lightly coats the back of a spoon.
Stir in the pumpkin puree, shredded cheeses, garlic powder, onion powder, salt, pepper, and chopped sage. Mix until the cheese melts and the sauce becomes creamy. Turn off the heat.
Add the cooked macaroni to the saucepan and fold until the pasta is evenly coated in the pumpkin cheese sauce.
Transfer the mixture to the prepared baking dish and spread into an even layer.
In a bowl, mix the shredded cheddar, breadcrumbs, olive oil, thyme, and chopped sage. Sprinkle the mixture evenly over the pasta.
Bake for 20 to 25 minutes until the topping is golden and crisp. Let it rest for 5 to 10 minutes before serving so the sauce can set.