Step 1 - Preheat the oven to 400 degrees F.
Step 2 - Grease a 9x13-inch baking dish with 1 tablespoon of the melted coconut oil.
Step 3 - Combine 2 tablespoons of the coconut oil, the butternut squash, the apple, the red onion, the sage, and the thyme in a large mixing bowl.
Step 4 - Season the squash mixture with the salt and the pepper, tossing to combine.
Step 5 - Transfer the squash mixture to the prepared baking dish, spreading it into an even layer.
Step 6 - Roast the squash mixture in the oven until the squash is fork tender, about 25-30 minutes.
Step 7 - Heat a large sauté pan over medium heat.
Step 8 - Add the bacon to the hot pan and cook, stirring occasionally, until the bacon is cooked through and crispy, about 8-10 minutes.
Step 9 - Transfer the bacon to a small mixing bowl lined with paper towels to drain, blotting off the remaining grease on top.
Step 10 - Discard the paper towels once the bacon has cooled, about 5 minutes.
Step 11 - Add the remaining coconut oil, the pecans, the honey, the cinnamon, and the cloves to the bacon mixture, stirring to combine.
Step 12 - Season the pecan mixture with the salt and the pepper, tossing to combine.
Step 13 - Top the squash mixture with the bacon-pecan mixture.
Step 14 - Roast until the topping is nicely browned, about 10 minutes.
Step 15 - Let cool for 5 minutes.
Step 16 - Serve.