Preheat your oven to 375 degrees. Cut the acorn squash in half lengthwise and scrape out the seeds. Brush with olive oil, salt and pepper. Place face-down on a large baking pan and add two teaspoons of water to the pan.
Bake squash for 35 minutes. Remove from oven and set aside.
While the squash bakes, bring a large stock pot of water to boil. When boiling, cook the noodles until al dente (10-15 minutes). Strain and set aside.
To make the cheese sauce, melt butter in a large sauce pan on medium heat. Add flour and whisk to combine. Then slowly add milk and heavy cream, whisking until combined. Heat mixture until it bubbles over medium heat (~5 minutes).
Reduce heat to low and add in cheeses. Stir until melted. Then pour the sauce over the macaroni and mix to combine. Let sit for a few minutes to thicken.
Flip over squash so that they’re face-up. Spoon as much macaroni into the squash. Feel free to top with mozzarella, then return to the oven and bake for 15 minutes.
Serve and enjoy!