Apple Butternut Squash Casserole with Bacon and Pecan Topping
When I first made this apple butternut squash casserole, it was to serve it as a holiday side. It’s got all of the best fall flavors and feels. But then I made it again outside of the holidays, and it dawned on me: this casserole is so good that it deserves a starring role on my table yearround. Plus, it’s so hearty and filling, it could be the main course.

Apple Butternut Squash Casserole with Bacon and Pecan Topping
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This casserole manages to combine quite a few traditional fall flavors into one outstanding dish. You’ll find apple, butternut squash, pecans along with spices like cinnamon and cloves. The thick-cut bacon brings out the salty-sweet flavors in this dish perfectly and adds enough protein that it would be perfect for a weeknight meal or on its own. It’s the perfect combo of sweet and savory and, frankly, the epitome of comfort food.

Ingredients
To make this dish, you’ll need
- 1/4 cup coconut oil, melted, divided
- 3 cup butternut squash, cubed
- 2 medium firm apples, cubed
- 1 small red onion, chopped
- 1 1/2 teaspoons fresh sage, chopped
- 1 1/2 teaspoons fresh thyme leaves
- 6 slices thick-cut bacon, chopped into ½-inch pieces
- 1/2 cup pecans, roughly chopped
- 2 tablespoons honey
- 1/2 teaspoon ground cinnamon
- 1/4 teaspoon ground cloves
- Sea salt, to taste
- Black pepper, to taste

Instructions
- Preheat oven to 400 F and grease a 9×13 baking dish with 1 tablespoon melted coconut oil. Set aside.
- Combine the butternut squash, apples, red onion, 2 tablespoons melted coconut oil, sage, and thyme in a large mixing bowl. Season with salt and black pepper, to taste, and toss to combine.
- 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.
- 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.
- Once cooled, discard the paper towels and add the remaining tablespoon of coconut oil, chopped pecans, honey, cinnamon, and ground cloves. Season with salt and black pepper, as desired, and toss to combine.
- 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!
Notes
You can use fresh butternut squash in this recipe, if it is the right time of the year to harvest from your garden. Or you can use frozen butternut squash. No need to thaw.
Made bacon in the air fryer and have leftovers? You can use that in this recipe, too. That’s an easy substitute.


Apple Butternut Squash Casserole with Bacon and Pecan Topping
Equipment
Ingredients
- 1/4 cup coconut oil melted, divided
- 3 cups butternut squash cubed
- 2 apples cubed
- 1 small red onion chopped
- 1.5 teaspoons fresh sage chopped
- 1.5 teaspoons fresh thyme leaves
- Sea salt and black pepper to taste
- 6 slices thick-cut bacon chopped
- 1/2 cup pecans roughly chopped
- 2 tablespoons honey
- 1/2 teaspoon ground cinnamon
- 1/4 teaspoon ground cloves
Instructions
- Preheat oven to 400 F and grease a 9×13” baking dish with 1 tablespoon melted coconut oil. Set aside.
- Combine the butternut squash, apples, red onion, 2 tablespoons melted coconut oil, sage, and thyme in a large mixing bowl. Season with salt and black pepper, to taste, and toss to combine.
- 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.
- 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.
- Once cooled, discard the paper towels and add the remaining tablespoon of coconut oil, chopped pecans, honey, cinnamon, and ground cloves. Season with salt and black pepper, as desired, and toss to combine.
- 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!
Notes
Nutrition
Disclaimer
Please note that nutrient values, if included with the recipe, are estimates only. Variations can occur due to product availability/substitution and manner of food preparation. Nutrition may vary based on methods of origin, preparation, freshness of ingredients, and other factors.
