And now, to bake your spaghetti squash in the oven … (scroll down for microwave directions). Heat oven to 375 degrees. Brush the inside of each half with olive oil and sprinkle with coarse salt and freshly ground black pepper. Place cut-sides down on a baking sheet.Bake for about 40 minutes until you can easily pierce the squash with a fork. Let cool for about 15 minutes, or until squash is cool enough to handle. With a fork, scrape out the spaghetti-like strands and prepare as desired.lace squash cut-sides-down in a microwave-safe baking dish. Fill the dish with about 1 inch of water. Microwave on high for about 12 minutes, or until you can easily pierce the squash with a fork.