Cut each acorn squash into quarters lengthwise; remove and discard seeds and membranes. Sprinkle squash evenly with salt and pepper. Place, cut sides down, on an aluminum foil-lined baking sheet coated with cooking spray.
Bake at 400° for 45 minutes or until squash is tender.
Combine butter, brown sugar, and nutmeg. Turn squash, cut sides up, on baking sheet; sprinkle evenly with butter mixture. Bake 5 to 7 more minutes or until brown.