Preheat the oven to 400 degrees. Line a baking pan with aluminum foil or parchment paper. Cut the squash in half, lengthwise and scoop the seeds. Place the halves, flesh side down, on the pan. Bake for about one hour or until the flesh is tender. When the squash is cool enough to handle, scoop the flesh into a large bowl.

While the squash is baking, pour the olive oil into a saute pan over low-medium heat. Cook the onion and garlic for 1-2 minutes, stirring occasionally, or until softened. Spoon the softened vegetables into the bowl with the squash. Add the cream cheese chunks and work them into the squash flesh using a wooden spoon. Add the eggs and stir the ingredients until the eggs and cream cheese are thoroughly incorporated. Mix in the sage, salt and pepper.

Spray 2 24-piece mini-muffin pans with cooking spray. Spoon equal amounts of the squash mixture into each of the hollows. Bake for 30 minutes or until the squash muffins are lightly browned.