Butternut Squash Enchilada Casserole (vegan + gluten-free)
Butternut Squash Enchilada Casserole- roasted butternut squash layered between tortillas with black beans, baby spinach, peppers, and enchilada sauce. Makes for a crowd pleasing casserole that’s easy to prepare!

If you like eating enchiladas but don’t enjoy the process of making enchiladas, then you’re going to love this butternut squash enchilada casserole.
Not only is it stuffed with nutritious seasonal vegetables but it is so much easier to make than traditional enchiladas. Let me show you how!

Butternut Squash Enchilada Casserole Ingredients
- Butternut Squash- As the highlight of the casserole, butternut squash offers a mildly sweet and nutty flavor. If you’re not into that, peeled and diced sweet potato would make a good substitute.
- Onion & Peppers- Along with the squash, we’re roasting onions and peppers for depth. I used poblano peppers but you can also use jalapeños or bell peppers.
- Cumin- To keep things simple, we’re sticking with cumin for our main seasoning. But feel free to add chili powder and/or smoked paprika if you really want to amp up the flavor.
- Tortillas- I prefer corn tortillas here as I find they hold up the best when covered in sauce, but any kind will work.
- Cilantro- Hate cilantro? No worries, just leave it out.
- Baby Spinach- I’m always looking for ways to sneak in greens but this ingredient is totally optional.
- Enchilada Sauce- Be sure to choose your preferred spice level for the sauce. Enchilada sauce or salsa both work well here.
- Black Beans- For fiber, protein, and antioxidants. Pinto beans would be also be good here.
- Shredded Cheese- I used Violife dairy-free shredded cheese to keep the recipe vegan.

How to Make Butternut Squash Enchilada Casserole
- Peel the squash. Slice off the bottom and the stem, then cut the squash in half lengthwise. Scoop out the seeds. Dice squash into 1-inch cubes. Side note: if the whole peeling and cutting squash thing seems like too much, you can always buy it already cut. No one is judging you.
- Roast the squash with the onions, peppers and cumin for about 45-minutes. Remove from dish.
- Layer sauce with quartered tortillas in the baking dish. Top with spinach, roasted vegetables, black beans, more sauce and shredded cheese. Repeat that step one more time.
- Bake in oven for 20-minutes, until heated through. Serve warm and enjoy!






Serving Suggestions
We like to top it with diced avocado, a drizzle of plan yogurt and chopped cilantro. Feel free to add cooked meatless crumbles or vegan chicken to amp up the protein!
More Butternut Squash Recipes to Try
- Butternut Squash Wild Rice Stew
- Butternut Squash Sweet Potato Soup
- Roasted Butternut Squash Lentil Curry
- Butternut Squash Pear Soup
- Butternut Squash Quinoa Chili
- Butternut Squash and Kale Risotto

Butternut Squash Enchilada Casserole
Ingredients
- 1½ cups 1-inch cubed butternut squash, from 1 medium-sized squash (approx 2lbs)
- 1 yellow onion, thinly sliced
- 2 poblano peppers, thinly sliced (can sub jalapeños or bell peppers)
- 1 tablespoon high heat oil (or oil spray), such as avocado oil
- 2 teaspoons ground cumin
- 16 ounces enchilada sauce, or salsa
- 1 15-ounce can black beans, drained and rinsed
- ¼ cup chopped cilantro, optional
- 8 tortillas, cut into quarters; I use corn tortillas
- 2 ounces baby spinach, roughly chopped
- 1¼ cup Mexican-style shredded cheese, I use Violife to keep the recipe dairy-free
- salt & pepper, avocado, plain yogurt and cilantro , for serving
Instructions
- Preheat the oven to 400°F. In a 9x13-inch baking dish, arrange the cubed butternut squash, thinly sliced onion and peppers. Drizzle (or spray) with high heat oil and sprinkle with cumin. Toss until evenly combined. Roast vegetables in the oven for about 45 minutes, or until the squash is tender. Remove baking dish from oven then lower temperature to 350°F.
- Transfer the roasted vegetables to a large bowl along with the drained and rinsed black beans, ½ cup enchilada sauce/salsa, and ¼ cup chopped cilantro.
- In the same 9x13-inch baking dish, prepare the casserole by spreading a thin layer of the salsa along the bottom. Using ½ of the quartered tortillas, layer the bottom of the baking dish. Top the tortillas with ½ of the chopped baby spinach, ½ of the roasted vegetables/black beans, and ½ cup of the enchilada sauce/salsa. Sprinkle ½ cup shredded cheese on top.
- Layer the remaining tortillas on top of the vegetables, followed by the remaining baby spinach, roasted vegetables/beans, remaining enchilada sauce/salsa and remaining shredded cheese. Bake in the oven for 20 minutes, until golden on top. You can broil the cheese for the last couple of minutes, if desired, to make it golden and bubbly.
- Allow the casserole to cool for 5-10 minutes, then cut into squares and serve. Season with salt & pepper, to taste. Garnish with avocado, plain yogurt and more cilantro, if desired. Enjoy!





Hello! I’m making this right now, and excited about trying it. Unfortunately, I’m fresh out of corn tortillas (and fresh out of time to run to the store). Would this work with flour tortillas?
Yes! You could use flour tortillas. They will probably be a little mushier than corn tortillas but toasting them first helps!
Thanks Izzy! I am feeling much better. Damn flu shot. ;)
Thanks Lauren! I hope you enjoy it! :)
Just made this and it came out awesome! Seriously butternut squash just upped my enchilada game to the next level. Thank you!!!
Woo hoo! So happy to hear that, Alyssa! Thanks for letting me know! :)
I just wanted to say this was soo delicious! I didn’t have spinach on hand so I substituted it with brussel sprouts. Turned out to be an excellent addition :)
Oh I love the idea to use brussel sprouts!! That sounds so good. I’ll have to give it a try. Thanks Raquel! :)
Do you know of a substitute to use in lieu of tortilla chips? May I use lasagna noodles instead? Any thoughts? Looks phenomenal though.
The recipe calls for tortillas not tortilla chips. But if you wanted to use lasagna noodles, you definitely could!
HI Sarah, I’m new to your blog and Love what I’m seeing! I was wondering if you think it would be possible to freeze this before baking? I will definitely be trying this!
Hi Therese! I’m so happy you found me. :)
I haven’t tried freezing it yet but I think it would work well. Let me know if you end up trying it!
I was looking for “fall-themed casseroles” for brunch this past Sunday and stumbled across your site and this recipe. I made this for my whole family and everyone RAVED (including me!!). I wasn’t sure how I would like the butternut squash in a Mexican dish, but it added a yummy sweetness that was to die for.
Altered this a little:
Used corn tortillas, not flour…. just left them whole and layered them
Added a can of yellow corn mixed with poblano peppers
Omitted the cilantro (yep, I have the I-hate-cilantro gene!)
Definitely added the spinach
Wowzers! Even my boyfriend who’s not a “foodie,” raved.
I’ll be making this again for sure!! Thank you for the wonderful recipe!!
Awesome! That makes me so happy to hear. Thanks Susan!
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Can I freeze leftovers?
Hi Michele! I haven’t tried to freeze this recipe but I think it would work okay. Let me know if you give it a try!
I made your wonderful butternut squash enchilada casserole today along with a vegan chilaquiles with chickpeas recipe from the vegan richa. Wow! Your recipe is truly delicious and a big hit around here. The two dishes compliment one another really well too. I intend to freeze portions for later use. Thanks for the great recipe, it is a new favorite around here!
That makes me so happy to hear, Charlie! I’ll have to look up those chilaquiles. They sound delicious! :)
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Just made this for dinner tonight — so good!
Only change was to omit the cilantro (ick! Don’t do that stuff!)
We are sad that it makes 9 servings, though. Wishing we could justify much larger servings!
But — super glad to have leftovers for the week ahead.
Flavor is incredible, and the inclusion of the spinach and the squash is wonderful.
Thanks for a great recipe.
I’m so happy you enjoyed it, Cindy! I know cilantro isn’t for everyone so I’m glad to hear it was still good without it. Thanks for the feedback!
Made this tonight for my family. It’s tricky cooking for a vegetarian daughter when the rest of us are meat-eaters. But, this butternut squash casserole was a huge hit with everyone. I used enchilada sauce and left out the cilantro–absolutely delicious!
I’m so glad to hear that everyone enjoyed this recipe. I can imagine that is very challenging for you to find a happy balance with everyone. Thank you so much for the feedback, Rebecca!
Can I make this ahead of time and feeeze?
Hi Jen! I haven’t tried freezing it but I think it would work okay. Let me know if you do!
I just made this tonight and loved it!! My husband was surprised how much protein it had for being vegetarian! Woohoo. Win for the wife. Any idea why it’s so high in sodium??
So happy to hear you and your husband enjoyed it, Colleen! The sodium content will vary depending on what specific kind of cheese, enchilada sauce/salsa, tortillas and beans you use. If you want a more accurate estimate, you can go to MyFitnessPal.com and enter in the exact brands you used. I hope that helps!
Has anyone tried a green sauce version of this recipe?
I haven’t but I think that would be delicious! Please let us know if you give it a try!
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I made this tonight with a few substitutions! I was in a time pinch after staying late for work (I work in healthcare too!), but this was on my menu for the week and leftovers for tomorrow so I had to cut a few corners- and it turned out great!
I peeled and cubed the butternut squash and put it in the bottom of a 9×13 pan, sprinkled chopped onions and 1 Roma tomato I had laying in my fridge I didn’t want to waste. I used 1 lb lean ground turkey and browned it then sprinkled on top, followed by the black beans. I covered in enchilada sauce and cheese. I then covered in foil and cooked 45 minutes at 400.
Delicious!
Do you think I could use frozen butternut squash and roast that. Cutting up butternut squash is quite the task.
Hi Maria! I haven’t tried roasting butternut squash so I’m not sure. My only concern would be if it becomes mushy then it might affect the texture. If you can find precut fresh butternut squash, that would probably work best!
Made this last night because I had a butternut squash that needed to be eaten. WOW! It was so good! My 2 year old ate 2 bowls full!
I love hearing this! Thank you for the review, Emily!
Did anyone try adding hamburger
Yes I use lean ground turkey and it’s amazing
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This is amazing.
Hi Sarah! Although I have enjoyed some absolutely wonderful recipes for over the years, I have never felt compelled to comment…until now! Your creation, combining the butternut with all the ingredients, was beyond delicious! At the end of preparing the dish I remembered a comment my husband had made regarding a dish I made with butternut squash….and that was,”It’s good babe but the squash has a sweetness to it.” He doesn’t care for sweetness in his food, wants to keep sweet for desserts. Soooo I became apprehensive with this dish. No need for worry because hubby loved it! Whew! We both loved it so much that hubby and I ate OVER half the casserole! Yep. Bellies have been stretched but oh so worth it . Thank you!
I’m so glad to hear that! Thank you for the kind comment, Linda!
I’m not a vegetarian but do like to incorporate healthy DELICIOUS meatless recipes into my meal rotation. Man, this recipe did not disappoint! I made it as written, using red enchilada sauce and corn tortillas. The only change I would make next time is cutting the squash into smaller chunks. I’ll definitely be making this again.
I love hearing that! Thanks Amy!
One of my favorites and family loves it as well! Very healthy and a comfort food to say the least!
Could this be prepared ahead of time? Thanks!
You could prepare it ahead of time and then cook it once you’re ready to serve. That could make the tortillas a little mushy…I’m not sure because I’ve never made it in advance. But it’s worth trying!
Also I’m thinking I’ll use pre-cut butternut squash to save time — how many cups should I use?
2 cups should be enough!
I don’t remember how I found this recipe, but this is become my go to recipe to impress my non-vegetarian friends. It is just so yummy and filling and flavourful. Tonight I split the recipe into five smaller containers. One for me for dinner, and for to freeze. So I can send to back to school with each of my kids at University.
I just wonder if enchilada sauce is certified gluten-free. If so, then with vegan cheese, I could make this for my celiac vegan friend. And he would love it.
This was delicious! My husband is vegetarian and I am not so I am always looking for recipes that we would both like. This dish has so much flavor and a little heat from the peppers. This recipes is definitely a keeper!
Delicious! Takes a bit of time to prep, but well worth it-never thought of using our home grown Red Kuri squash in an enchilada casserole, but it works so well, and Mexican flavors are always the best! Thank you so much for posting.
This was delicious!!! I used enchilada sauce instead of any chili peppers or salsa and put a little Rotel tomatoes on the top layer. I love black beans but I substituted pinto beans for my husband. I am vegan so I used real cheese on one side for my husband and vegan on the other. He was skeptical but loved it! I bet you could use potatoes instead of the squash, too!
Great recipe! I have swapped cannelli beans for black beans and added roasted red peppers for colour. I have made it for vegan friends without the cheese. It is still delish. I also decorate the top with corn tortillas cut into triangles and stuck in each serving size. These are fun and good for slopping up guacomole toppings. One of my go to recipes now!
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Thanks for a great recipe! I made this for the first time last night. I’m vegetarian, and my husband is gluten free, so I’m always looking for new ideas to feed us both! My husband loved it!
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I just made this today.. hands down one of the best things I have ever eaten! My husband was skeptical, now he cant stop eating it!! I love it so much I even portioned some out for my friends and family because I know they will love it too!!!
I make this regularly. It is incredibly simple and delicious! My family loves it!
Love this recipe! Have made it several times for family and friends and it’s a perfect fall dish for anyone who’s a fan of a little Mexican inspiration!
My God I want to eat the entire pan! This is so delicious I will be making this weekly Taco Tuesday is now enchilada casserole Tuesday.
I made this recipe today and it was very delicious. I followed the recipe except I did not have cilantro so I substituted green onions. Also, I did not use poblano or jalapenos. But used green bell pepper and added a little more cumin. My husband ate 2 servings. We both loved it and I will be making it again. A little time consuming to prep but worth it.
This looks so good! What a fun way to make this dish for fall !
Thanks for sharing! Does it keep long?
Hi! I am so excited for this recipe. Any tips for using frozen butternut squash that doesn’t go mushy? I convinced myself to buy a huge bag of it while at Costco but haven’t had much luck with making it in a non-mushy way :)
Thanks!
That’s a tough one! Roasting it should help dry it out a bit but there’s still a chance it will be mushy. I would recommend using it for a pureed butternut squash soup or pasta sauce :)
This was very good. Family loved it.
I have been making this recipe every fall for years now and it continues to be a favorite! I buy squash every year specifically for this recipe. Thank you!!
Thank you so much for the review! :)
Very disappointed in this dish. Will not make again. I did not use the amount of heat called for and it was still too hot for me. The tortillas were a mix between too hard or too soft and the dish was on the dry side, needs a bit of sauce.
I needed a more keto-friendly recipe, so I used delicata squash (no need to peel and you only need to scoop the seeds and cut it up) instead of butternut, 1.5 pounds of lean ground beef (browned and seasoned with a bit of fajita seasoning) and the egg and cauliflower tortillas instead of the corn. It came out great.
First, I have to admit that I didn’t follow the recipe in that I didn’t want the stodgy carbs, so left out the tortillas and instead roasted thin slabs of butternut squash and added corn to the roasted vegetable mix. The butternut squash slabs were used instead of tortilla and overall, I was very happy with the results! Thank you for the recipe!
Love this delicious looking Butternut Squash Enchilada Casserole- roasted recipe. I Never tried this before but will surely gonna try this one , Super excited !!!!!!
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This looks so good! What a great combination of flavors for fall!
Thanks for sharing! Does it freeze well?
I’ve made this recipe a dozen times, usually for guests, served with grilled beef or chicken and a green salad. It’s so delicious and seems to be something my guests have never made and they love it. I always send them home with leftovers. I get pictures texted of them eating it for breakfast the next day. Pretty funny. A hearty vegetarian crowd-pleaser.
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Second, this is an amazing recipe, very similar to my own with a few tweaks I greatly appreciate. But I won’t be back for more. Really too bad for both of us.
I’m sorry you’re having issues with ads! I actually use my site all of the time to cook from myself and rarely have issues. What browser are you using?