Apple Butternut Squash Casserole is everything cozy comfort food should be. This warm, savory-sweet dish layers tender roasted butternut squash with juicy apples and a touch of smoky bacon, all baked beneath a crispy, golden topping. It’s a unique blend of autumnal flavors that pairs beautifully with hearty main courses or stands out on its own.

This casserole isn’t just about flavor—it’s about texture, too. You get the softness of roasted squash, the juicy bite of apple, and the crunch of the crisp bacon and topping. It’s a crowd-pleaser at fall gatherings, holiday dinners, or even a cozy weeknight meal. One pan, loads of flavor, and a seriously satisfying bite every time.

What Kind of Apples Should I Use?

You want apples that hold their shape when baked but also add natural sweetness. Honeycrisp and Fuji apples work beautifully in this casserole. They don’t turn to mush and offer the right amount of tart-sweet balance to complement the earthy squash.

Ingredients for the Apple Butternut Squash Casserole

Butternut Squash: This is the base of the dish. Its natural sweetness and creamy texture after roasting give the casserole body and warmth.

Apples: Choose firm, slightly sweet apples like Honeycrisp or Fuji to balance the savory and add juicy contrast.

Bacon: Adds a smoky, salty crunch that lifts the flavor of the dish and provides richness.

Onion: Caramelized onion brings a savory depth that cuts through the sweetness of the apples and squash.

Butter: Used for sautéing and flavor, adding a luxurious richness.

Brown Sugar: Just a hint helps enhance the sweetness of the squash and apples.

Fresh Thyme: Earthy and herby, thyme is a perfect match for both squash and apples.

Crispy Fried Onions or Panko Crumbs: This forms the crunchy topping that gives the casserole its irresistible finish.

Salt & Pepper: Essential to bring balance and round out all the flavors.

How To Make the Apple Butternut Squash Casserole

Step 1: Prep and Preheat

Preheat your oven to 375°F. While it’s warming, peel and cube your butternut squash and apples into similar-sized chunks for even cooking. Dice the onion and set everything aside.

Step 2: Sauté the Aromatics

In a large skillet over medium heat, melt butter and add the diced onion. Sauté until the onions are soft and caramelized, about 8–10 minutes. Add a pinch of salt and pepper to enhance the flavor.

Step 3: Crisp the Bacon

In a separate pan, cook the bacon until crispy. Drain on paper towels, then crumble and reserve for topping.

Step 4: Layer the Ingredients

In a greased 9×13 baking dish, layer the cubed butternut squash and apples. Spoon the caramelized onions evenly over the top. Sprinkle lightly with brown sugar, fresh thyme, and a bit more salt and pepper. Dot with a few small cubes of butter for extra richness.

Step 5: Bake Until Tender

Cover the baking dish with foil and bake for about 30 minutes, or until the squash is tender when pierced with a fork.

Step 6: Add the Crunchy Topping

Remove the foil and sprinkle the casserole with crispy fried onions or panko crumbs, and the crumbled bacon. Return to the oven uncovered for another 10–15 minutes, or until the top is golden brown and crisp.

Step 7: Garnish and Serve

Garnish with extra thyme if desired and serve warm. It pairs beautifully with roasted meats or a crisp green salad for a lighter option.

How to Serve and Store Apple Butternut Squash Casserole

Apple Butternut Squash Casserole is best served warm, straight from the oven when the topping is at its crispiest. It makes a perfect side dish for roasted chicken, turkey, or even pork chops. You can also enjoy it as a vegetarian main (just skip the bacon), paired with a slice of crusty bread or a crisp fall salad.

To store, let the casserole cool completely, then cover and refrigerate for up to 4 days. To reheat, pop it in a 350°F oven uncovered for 15–20 minutes to restore the crunch, or microwave individual servings for a quick warm-up (though the topping may soften a bit).

Frequently Asked Questions

What if I don’t have butternut squash?

You can substitute with sweet potatoes or acorn squash. Both offer a similar sweetness and texture.

Can I make this casserole ahead of time?

Yes! You can assemble it (without the crunchy topping) up to a day in advance. Just cover and refrigerate, then bake when ready.

Is it freezer-friendly?

Absolutely. Freeze the baked (and cooled) casserole in an airtight container for up to 2 months. Reheat in the oven until hot.

Can I make this vegetarian?

Yes, just skip the bacon or replace it with a plant-based alternative. You could also add toasted pecans for extra texture.

What kind of apples work best?

Stick to firm apples like Honeycrisp, Fuji, or Gala. They hold their shape well and offer a nice balance of sweet and tart.

Can I double the recipe?

Definitely. Just use a larger baking dish or two separate ones and adjust baking time slightly.

Want More Comfort Food Casserole Ideas?

If this Apple Butternut Squash Casserole hit the spot, you’ll love diving into these cozy, flavorful dishes next:

• Cheesy Broccoli Rice Casserole for a creamy, veggie-packed classic.
• Funeral Potatoes full of cheesy goodness and crunchy topping.
• Bacon Egg and Hash Brown Casserole perfect for breakfast-for-dinner nights.
• Crab Casserole if you’re in the mood for something rich and seafood-inspired.
• Gooey Cinnamon Roll French Toast Casserole when your sweet tooth kicks in.

📌 Save this recipe to your Pinterest fall or holiday board so it’s right at your fingertips when the craving hits.

And hey—let me know how yours turned out! Did you try a different type of apple or go for a vegetarian version? Maybe you added nuts or a drizzle of maple syrup?

I love hearing how these recipes come to life in your kitchens. Drop a comment or question below, and don’t forget to check out more daily recipes on my Pinterest: Life with Nina

Apple Butternut Squash Casserole

Author: Nina Johnson

Print Recipe

Description

This Apple Butternut Squash Casserole is the perfect blend of savory and sweet, combining roasted butternut squash, tender apples, caramelized onions, and crispy bacon. Topped with crunchy fried onions or panko, it’s a comforting, crowd-pleasing side dish for fall dinners and holiday gatherings.

Instructions

1. Preheat oven to 375°F. Peel and cube the butternut squash and apples into similar-sized chunks. Dice the onion and set aside.

2. In a skillet over medium heat, melt butter and sauté diced onions until caramelized, about 8–10 minutes. Season with a pinch of salt and pepper.

3. In a separate pan, cook bacon until crispy. Drain and crumble.

4. In a greased 9×13 baking dish, layer squash and apples. Top with sautéed onions, brown sugar, thyme, additional salt and pepper, and a few butter cubes.

5. Cover with foil and bake for 30 minutes, or until squash is fork-tender.

6. Remove foil, sprinkle with crispy onions or panko and crumbled bacon. Bake uncovered for 10–15 more minutes until golden and crisp.

7. Garnish with more thyme and serve warm.