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Apple Butternut Squash Casserole in baking dish on a burlap mat
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Apple Butternut Squash Casserole with Bacon-Pecan Topping

This Apple Butternut Squash Casserole with Bacon-Pecan Topping is a perfect Fall food side dish.  It would make a delicious addition to your holiday menus .


  • 1/4 cup coconut oil, melted, divided
  • 3 cups butternut squash, peeled, seeds removed, and cut into 1 inch cubes
  • 2 medium Honeycrisp apples, cored and chopped into 1 inch cubes
  • 1 medium red onion, roughly chopped
  • 1 1/2 teaspoon fresh sage, chopped
  • 1 1/2 teaspoon fresh thyme
  • salt and pepper, to taste
  • 6 slices thick-cut bacon, chopped into 1/2 inch pieces
  • 1/2 cup pecans, roughly chopped
  • 2 tablespoons honey
  • 1/2 teaspoon ground cinnamon
  • 1/4 teaspoon ground cloves


  • You will need to peel the butternut squash, cut it in half - lengthwise and scoop out all of the seeds.  Then it's a matter of cutting it into one inch cubes.  A time-saver tip would be to buy already cubed squash from the produce section in the grocery store.  
  • Once you have your squash cubed you can preheat your oven to 400 degrees and grease your 13" by 9" baking dish with one tablespoon of melted coconut oil.  
  • Then core your apples and chop them up into one inch cubes.  You can peel the apples if you prefer, though it's not necessary. I like to use a Honeycrisp apple but your favorite will work as well. 
  • Place squash and apples in a large bowl.  Rough chop your onion and then add it to the bowl.  Add 2 tablespoons melted coconut oil, sage, and thyme to the squash mixture.  Season with salt and black pepper, to taste, and toss to combine.
  • Transfer the butternut squash mixture into your prepared baking dish and spread into an even layer.  Roast in the oven just until the butternut squash is fork tender, around 25-30 minutes.
  • While the apples and squash are roasting, prepare your topping by frying up the bacon.  Heat a large skillet 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 plate lined with paper towels to absorb excess grease. Blot off remaining grease on top and set aside to cool for 5-10 minutes.
  • Once the bacon is cooled, crumble it into large pieces and place it in a small bowl.  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. 
  • When the squash is done, remove 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.