What says Fall is here more than Apple Butternut Squash casserole? How about when you make an Apple Butternut Casserole- if that isn’t yummy enough, add some Bacon on the top! Sounds amazing, doesn’t it? And, it’s Paleo-friendly!
When it comes to fall comfort food, this Paleo Apple Butternut Squash Casserole with Bacon-Pecan Topping checks every box — sweet, savory, and satisfyingly cozy! 🥰 It’s the kind of side dish that brings all the flavors of autumn together in one bite: roasted butternut squash, crisp apples, smoky bacon, and crunchy pecans. Whether you’re following a paleo lifestyle or simply love wholesome, real-food recipes, this casserole is guaranteed to steal the spotlight at your holiday table.
It’s the perfect dish for Thanksgiving, Friendsgiving, or any cozy weekend meal. The combination of naturally sweet squash and apples with that irresistible bacon-pecan topping gives it a comfort-food feel with a healthy twist. Serve it warm and watch everyone go back for seconds — it’s proof that paleo can be anything but boring! 🍂✨
More Casseroles you’ll love:
When it comes to side dishes, it’s really hard to get away from the basic veggies. However, for a yummy change of pace, I have an easy Broccoli Casserole recipe that I am sure you will love! I even have family members who refuse to eat broccoli that love this simple recipe!
If you love delicious potato recipes, then you simply cannot go wrong with this Loaded Mashed Potato Casserole recipe! It is super easy to make and loaded with delicious flavors. It is also guaranteed to become a family favorite!
Prep time: 15 minutes
Cook time: 35-40 minutes
Serves: 4-6
Ingredients:
¼ c. coconut oil, melted, divided
3 c. butternut squash, cubed
2 medium firm apples, cubed
1 small red onion, chopped
1½ t. fresh sage, chopped
1½ t. fresh thyme leaves
Sea salt and black pepper, to taste
6 slices thick-cut bacon, chopped into ½-inch pieces*
½ c. pecans, roughly chopped
2 T. honey
½ t. ground cinnamon
¼ t. ground cloves
*Use Paleo-friendly bacon to keep this recipe compliant.

Directions:
- 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 pre-heated 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!



