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Preheat oven to 400°F and grease a 9x13” and spray with nonstick spray. Set aside.
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Combine the butternut squash, apples, red onion, oil, sage, and thyme in a large mixing bowl. Season with salt and black pepper, to taste, and toss to combine.
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Transfer the butternut squash mixture onto the prepared baking dish and spread into an even layer. Place in the preheated oven to roast just until the butternut squash is fork-tender, around 25-30 minutes.
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While the butternut squash mixture is roasting, heat a large sauté pan over medium heat and add the bacon. Cook, stirring occasionally until the bacon is cooked through and crispy, approximately 8-10 minutes. Transfer the bacon to a small mixing bowl lined with paper towels to absorb excess grease. Blot off remaining grease on top and set aside to cool for 5-10 minutes.
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Once cooled, discard the paper towels and add the chopped pecans, honey, cinnamon, and ground cloves. Season with salt and black pepper, as desired, and toss to combine.
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Remove squash from oven and top with the bacon-pecan mixture. Return to the oven until the topping is nicely browned, approximately 10 minutes. Remove from oven and cool for 5 minutes before serving. Enjoy!