Baked Spaghetti Squash. 1  1. Preheat your oven to 350ºF (176ºC). 2  2. Add 1/4 inch of water to the baking sheet. 3  3. Bake the squash for 40-45 minutes.  4. Remove the squash with a 1  fork. 5. Spoon the mozzarella cheese, spaghetti sauce, and basil over the squash.  6. Bake the squash again until the cheese begins to 1  bubble. 7.  Serve.