Healthy Butternut Squash Apple Casserole

Butternut squash apple cranberry bake on a plate.

This Healthy Butternut Squash Apple Casserole is the perfect side dish to serve for any weeknight or holiday meal. Made with roasted butternut squash, apples and cranberries, this squash bake has just the right amount of sweetness and tartness to keep you running back for more! {Vegan, gluten-free & paleo}

A plate of butternut squash apple casserole next to beans and cranberries.

Healthy Squash Casserole

For several years now, we’ve been making this butternut squash apple casserole recipe (inspired by my mother-in-law’s famous dish) and it’s become a favorite holiday side dish for both the kids and grown ups!

Made with a mixture of butternut squash, apples, cranberries and a delicious maple cinnamon glaze, this casserole recipe is the perfect combination of sweet and tart.

Roasting the squash and apple accentuates their natural sweetness and gives them a buttery texture. It pairs so well with all of your favorite holidays dishes or as a delicious side dish for a fall meal!

My favorite thing about this butternut squash apple bake is that it’s a cinch to make and can be made ahead of time, so it’s an excellent side dish to prepare during the busy holiday season. You’ll want to make extras of this one because it definitely won’t last long!

For more healthy squash recipes, check out this Roasted Butternut Squash and Carrot Soup and Quinoa Salad with Pomegranate.

Healthy squash casserole with apples and cranberries in a rectangular baking dish.

Why We Love This Healthy Butternut Squash Casserole

This apple butternut squash casserole has just the right amount of sweetness from the apples and butternut squash, and tartness from the cranberries
Loaded with Vitamin A and C, dietary fiber and antioxidants to support your immune system, digestion, and overall wellbeing
Perfect healthy side dish for your holiday meal
Modern twist on a classic casserole, using maple syrup instead of a cinnamon-sugar glaze
Gorgeous colors and vibrant fall flavors
Can be prepared in advance
Tastes just as good, if not BETTER, as leftovers
Smells A-MAZING
Easy dairy free, gluten free, and vegan option

Ingredient notes

The ingredients for the squash casserole with labels

Ripe butternut squash: Use a large butternut squash. Peel and dice it into about 1-inch uniform sized pieces.
Apples: Thin slices of apple add a nice sweetness to the squash bake. Use an apple variety that is suitable for baking, such as Macintosh, Gala, or Honeycrisp apple. Try to avoid tart apples like Granny Smith apples since the cranberries will already be fairly tart.
Cranberries: Incorporate a bit of tartness that complements the sweetness of the apples and glaze. Use fresh or frozen cranberries.
Pure maple syrup: Provides sweetness to the casserole.
Melted coconut oil: Forms the glaze along with the maple syrup. Use unrefined for a mild coconut flavor or refined for no coconut flavor. You can also use butter if preferred.
Tapioca starch: Helps to thicken up the glaze mixture. You can also use cornstarch, or regular flour as a thickener.
Spices and seasonings: Cinnamon, nutmeg and sea salt add flavor to the casserole and bring out the sweetness of the apples and buttery flavor of the squash. Add more or less depending on your personal tastes.

How to Cut Butternut Squash

Use a large sharp chef’s knife to cut both ends off the squash.
Prop the squash upright with the bottom on a flat surface and cut in half lengthways. Make sure it’s fairly stable on a chopping board and keep your fingers out of the way.
Then, use a vegetable peeler or knife to remove the skin and scoop the seeds out with a spoon.
With the flat side down, cut the squash into strips and then dice into 1-inch cubes.

How to Make Butternut Squash with Cranberries and Apples

The butternut squash, apples and cranberries in a large white bowl

The squash, apples and cranberries tossed with spices in a large bowl with a wooden spoon

First, you’ll need to preheat the oven to 350°F. Peel the squash and apples (I love using th is peeler because it moves along with the grooves of the fruits and vegetables). Once peeled, cut the squash in half, remove the seeds and dice it into one-inch cubes. Next, thinly slice the apples. You can really use any type of apple that you prefer. Galas or Macintosh tend to work especially well for this recipe.
In a large mixing bowl, mix together the squash, apple slices and cranberries.
Add in the maple syrup, coconut oil, tapioca, cinnamon, salt, and nutmeg and toss to evenly distribute.
Place butternut squash mixture in an ungreased 7×11 inch baking dish (or a large rectangular baking dish) in an even layer. Cover with foil and bake casserole in the preheated oven for 35 minutes; then toss to ensure all components are cooked evenly. Place back in oven, and bake for an additional 30-35 minutes. Allow to cool for about 10-15 minutes to allow liquid to caramelize. Serve warm.

Close up of a spoon digging into the healthy butternut casserole with apples and cranberries.

Expert Tips

Look for squash with minimal bruising and no obvious cuts or areas that are oozing. The squash should feel heavy for its size.

Avoid cutting the chunks of squash too large, or they won’t finish cooking at the same time as the apple.

The cranberries tend to soften and burst while cooking. If you want your cranberries to stay more intact, add them in with the rest of the casserole in the last 20 minutes of cooking.

You’ll probably notice that when this bake comes out of the oven, there will be quite a bit of liquid at the bottom of the dish and that’s totally okay. Toss the squash, apples and cranberries so that they’re well coated in this mixture and then allow the dish to sit for about 15-20 minutes. This will give the mixture time to thicken slightly and caramelize. You can also drizzle some of the glaze on top of the squash casserole when dishing it out.

I highly recommend using the foil when baking the casserole as it helps prevent the liquid from evaporating and the casserole from drying out.

Bake the squash and apples until they’re tender enough that they can easily be pierced with a fork. This dish tastes best when everything is very tender and caramelized.

A plate of squash apple bake ready to be served.

Storage and Reheating Guidelines

Refrigerator: This apple squash casserole should last covered in the fridge for up to four days. You’ll notice that the glaze will thicken up a bit and form more of a caramel-like consistency once it’s been sitting in the fridge, but it still tastes amazing as leftovers the next day.

Freezer: Allow the casserole to cool completely after cooking. Remove from casserole dish and transfer to a freezer-safe airtight container. Freeze for up to a month.

How to Reheat

From frozen: Allow it to thaw in the fridge overnight. Transfer to a baking dish and bake in the oven at 350 degrees F for 15-20 minutes or until heated through.

From unfrozen state: Preheat oven to 350 degrees F. Place casserole in the oven for about 10 minutes or so or until heated through.

If you’d like a faster option, you can always place it in the microwave for a minute or so to warm it up.

Recipe FAQs

Do you peel squash before cooking?

Peeling a squash before cooking isn’t always necessary, but in this case, it’s highly recommended. We don’t want any chewy bits of skin in the casserole as the squash is meant to be very tender. For best results, peel the squash right before dicing the squash into cubes.

Is butternut squash casserole healthy?

Not every squash casserole is created equally, but this butternut squash casserole recipe is definitely a healthier option. Due to the presence of the butternut squash, apples and cranberries, it packs plenty of fiber in addition to vitamin A, vitamin C, potassium, magnesium and antioxidants.

It is also naturally vegan, gluten-free, and refined sugar-free, which is great for any family members or guests who might have specific dietary requirements.

A spoon holding up some of the butternut squash apple casserole.

Serving Suggestions

One thing I love about this butternut squash apple cranberry bake is that the flavors complement so many other holiday entrees and side dishes.

If you’re looking for a few ideas for Thanksgiving dinner or Christmas dinner, here are some to try out!

This squash bake pairs well with:

And so many more!

Recipe Variations

Different base: Try using acorn squash instead of butternut squash. Diced sweet potatoes would also work well.
For a buttery flavor: Sub in butter for coconut oil.
Sweetener: Use honey, coconut sugar or brown sugar instead of maple syrup.
For less tartness: Use all dried cranberries instead of fresh.
For a crunchy texture: Add a sprinkle of nuts such as pecans or prepare a bacon-pecan mixture to really bring it to the next level.

A fork picking up some of the butternut squash casserole from a plate.

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