Butternut Squash Enchilada Casserole (Freezable)

This butternut squash enchilada casserole bakes up with the bold spices of enchilada sauce, cheese, black beans, butternut squash and tortillas. Simple to assemble, and can be frozen for later!

While enchiladas are one of my favorite Tex-Mex foods, I find the process can be too labor-intensive for a weeknight dinner. Instead I opt for an enchilada casserole, which skips the rolling, but has the same delicious flavors.

Like my cauliflower rice enchilada casserole, this butternut squash enchilada casserole comes together quickly thanks to store bought enchilada sauce, tortillas, and just a handful of other ingredients. I think you’re going to love it!

Recipe video

Watch the video below for step by step instructions assembling and cooking this casserole! You can find more recipe videos on my YouTube channel.

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Ingredient notes

• butternut squash– for this recipe, we will need 6 cups of butternut squash cubes; this is roughly half of a large butternut squash. Cut them into 1 inch cubes.
• black beans– you can use canned black beans, or cook your own black beans in the Instant Pot or on the stove top.
• enchilada sauce– I have tested this recipe using La Victoria and Fronterra brands, and they both had the perfect amount of seasoning for this recipe. If you can’t find enchilada sauce, I love this homemade enchilada sauce recipe (without the salt). Make sure you use a boldly flavored enchilada sauce, as milder ones can result in a less flavorful casserole.
• tortillas– use corn or flour tortillas
• cheese– mozzarella is fairly neutral in flavor and gets nice and creamy in the casserole as it cooks. Swap for cheddar, monterey jack, or get fancy with jalapeno havarti

Recipe notes

Start by roasting the butternut squash

While this is a very hands off recipe, we do need to get the butternut squash roasting ASAP so that it cools slightly and can be mixed with the filling.

Toss the butternut squash cubes in olive oil, and season with salt and pepper. Spread it out on a baking sheet, and roast for 25 minutes at 425°F. Stir or flip the squash halfway through.

Once a fork inserts easily into the squash, remove from the oven and allow to cool for 15-20 minutes.

Assembling the filling

Once squash is cool enough to handle, mix it up with the black beans, enchilada sauce, and corn.

You can do this step ahead of time if you’d like to save time; store in the fridge for up to 4 days to make casserole assembly easy (I do not recommend assembling the casserole ahead as the tortillas get soggy).

Layering the casserole

This is a really ‘loosey goosey’ casserole that is layered similar to a lasagna. Don’t sweat the order too much, because like most casseroles, this comes out of the pan pretty messy, gooey and delicious.

Tortillas

Cut large tortillas into quarters, and arrange with the cut sides into the corners of a 9 x 9 inch baking dish. Overlap them so that little to no baking dish is uncovered. You can use smaller tortillas as well, but will need more of them to completely cover the bottom of the dish.

Filling

Next, layer half of the filling on top of the tortillas. Spread it flat across the top using a spatula so that it is even.

Cheese + Repeat

Sprinkle half of the cheese evenly over the casserole filling.

Repeat with a second layer of tortillas, filling and cheese. Your baking dish might be getting quite full, so be sure to press the filling mixture down if needed to maximize space. End with the layer of cheese, because it melts and makes for a great presentation.

Baking the casserole

Once assembled, you can bake this butternut squash enchilada casserole right away, or you can freeze for later.

Right away

Leaving the baking dish uncovered, bake in the oven for 20-30 minutes, until the cheese is melted and the casserole is bubbly and heated through. Let the casserole sit for 10 minutes before serving it up.

Baking from frozen

This casserole works incredibly well baked from frozen. To freeze, you will need to use a metal or disposable baking dish- do not freeze it in glass as extreme temperature shifts can cause glass to crack or shatter.

1. Cool the casserole to room temperature before covering with plastic wrap, then foil. Make sure to label with the date and baking directions (I write directly on the foil).
2. Freeze for up to 3 months.
3. When ready to bake, remove the plastic wrap, then cover back up with the foil (spray foil with oil before replacing it).
4. Place the fully frozen casserole into the oven at 350°F and bake for 1 hour.
5. Uncover and bake for another 20 or so minutes, until the cheese is melted and casserole is heated all the way through.

I actually recommend baking this casserole from frozen versus thawing before baking as it helps the tortillas keep a good texture and not get soggy.

To serve

This is just like enchiladas: best served with delicious toppings.

• green onions
• sour cream
• salsa
• avocado or guacamole
• tortilla chips
• fresh tomatoes

Storage + reheating

This casserole is best enjoyed within 48 hours of baking, as the tortillas can start to get soggy after that.

• fridge– cool the casserole completely, then cover and store the entire baking dish, or portion out single servings into your favorite meal prep containers. Store in the fridge for up to 4 days safely (but best enjoyed within 2 days)
• reheat- bake the entire casserole (uncovered) at 350°F for 20 minutes, or until warmed through. Heat individual portions in the microwave until steaming hot.
• freezer– I do not recommend freezing after baking through; I do recommend freezing before baking (see above- “baking from frozen”).

Find my favorite meal prep containers here!

More casserole recipes

• Mexican Spaghetti Squash Casserole
• Broccoli Quinoa Casserole
• Healthier Taco Casserole
• Chicken Caprese Pasta Bake
• Turkey Zucchini Lasagna