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Preheat oven to 375°F. Lightly coat a 2-quart rectangular baking dish with cooking spray; set aside.
In a medium microwave-safe bowl, combine squash and water; cover with vented plastic wrap. Microwave on High for 4 minutes; stir. Microwave, covered, about 4 minutes more or until squash is tender. Carefully remove plastic wrap. Mash squash; set aside.
Meanwhile, cook pasta according to package directions; drain. In a medium saucepan, melt butter over medium heat. Add mushrooms and green onions. Cook until tender, about 5 minutes. Sprinkle flour over mushroom mixture. Cook and stir for 1 minute. Add milk, salt and pepper. Cook and stir over medium heat until thickened and bubbly. Remove from heat; stir in squash. Add pasta; gently fold to combine.
Transfer half the pasta mixture to the prepared baking dish. Sprinkle with half of the cheese. Add remaining pasta and cheese. Top with bacon, if desired. Bake, uncovered, for 20 to 25 minutes or until heated through and cheese is melted. Top with additional green onions, If desired.