Butternut Squash Enchilada Casserole without Tortillas

by From Scratch Farmstead

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This butternut squash enchilada casserole is a delicious alternative to standard enchiladas, nourishing comfort food at its finest.  It can easily be made keto friendly without beans or vegetarian by substituting extra veggies for the meat. It is a perfect way to use that extra shredded meat from a roast or whole chicken or leftover roasted vegetables. And you’ll find butternut squash to be the perfect, tasty substitute for tortillas.

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Why We Love Enchilada Casserole!

Enchilada casserole is a family favorite, frequently requested on birthdays and special occasions. Swapping butternut squash for the tortillas increases the nutrients without compromising anything in the taste or texture. It is a great fall and winter dish that puts to use squashes that store well for months when seasons of green grass and fresh veggies from the garden are long gone.

Growing up, enchilada casserole was a dish that we busted out maybe once a year for a special occasion. Assembling it would be a family affair with cans upon cans lining the counter. Chili, enchilada sauce, beans, almost everything in the recipe was poured from a can.

Just a portion of our 2021 squash haul!

I’m always on a mission to take our favorite recipes and figure out how I can adapt them to pack them full of more nourishing, from scratch, and fresh ingredients. Once I discovered how to make a simple from scratch enchilada sauce, enchilada casserole was immediately on the menu.

Why We Use Squash

This year, our goal was to feed our family all year, as much as possible, through the food that we grew or raised. With this goal in mind, we emphasized growing crops that stored well through the winter and winter squashes ranked high on that list. We planted a large three sisters garden (corn, beans, and squash) and were delighted to harvest a couple hundred winter squashes come October.

Now, I’ve been trying to figure out creative ways to incorporate all of those beautiful, orange fruits into our cooking. Roasted, mashed, pancakes, baked, you name it, we’ve been doing it. When there was a request for enchilada casserole, I tried swapping the tortillas for butternut squash slices and the result was a resounding success.

This butternut squash enchilada casserole has three main layers that you alternate each three times: Butternut squash slices, filling, and cheese in addition to the enchilada sauce that is incorporated throughout. Our favorite way to eat the enchilada casserole is over a bed of Spanish rice or cauliflower rice. The rice absorbs the extra liquid in the butternut squash enchilada casserole and they pair beautifully. This recipe makes a hefty portion perfect for leftovers or when having guests for dinner.

The players:

Butternut Squash Slices – You’ll want these slices to be thin (roughly 1/8”) and uniform in width. The slicing attachment on a food processor or a mandolin slicer would make cutting these a breeze. However, my preference is still to slice them by hand with a sharp knife!

thin butternut squash slices

Filling – This part of the recipe is so versatile and where you have the chance to customize your casserole to your family’s preference. Beef, pork, chicken, fish, or vegetarian. Beans or no beans. Spicy or mild. Loaded with vegetables or more meat based. It’s all up to you. I’ll share our basic recipe where we used shredded beef, black beans, onions, peppers, and garlic, but feel free to adjust it to incorporate what you love. We have never made a combination we haven’t devoured.

Cheese –  We used a combination of mozzarella and cheddar because that is what we always have on hand but you can use whatever sliced or shredded cheese you prefer.

Enchilada Sauce – With a bone broth base, thickened by arrowroot starch and seasoned with tex-mex spices, this enchilada sauce recipe is an easy, nourishing alternative to the standard canned version and in our opinion really takes this recipe up a few notches. It avoids the top allergens making it a friendlier option for serving to a crowd without lacking any of the flavor. You can find the recipe here or our video.

laying butternut squash on casserole

Adding a layer of butternut squash.

Butternut Squash Enchilada Casserole without Tortillas Recipe

Ingredients:

Keep in mind this recipe is highly adaptable to what you have on hand, but here’s what we used:

1 medium butternut squash (sliced 1/8” thick)
3 cups shredded beef (or meat of choice)
1 onion, diced
1 pepper, diced
3 cloves garlic
4 cups black beans (or bean of choice)
3 cups shredded cheese
3 cups enchilada sauce
Spanish rice or cauliflower rice to serve casserole over (Optional)

How to prep and assemble your enchilada casserole:

Step one: Prepare three cups of your enchilada sauce. Here’s the recipe for our simple, from scratch version.

Step two: Make your filling. In this recipe, I used a combination of shredded beef from a chuck roast, black beans, onions, garlic, and peppers. Dice and sauté your onions, garlic, and peppers. After your veggies are cooked, stir in beef and beans. Pour and incorporate 1.5 cups of enchilada sauce into the filling mixture. Set aside.

Step three: Peel, seed, and slice your butternut squash into uniform slices (1/8”) either by hand or with a slicer. We use both the half circle and rainbow shaped portions – just adjust accordingly while laying on your pan so that it is fully covered as much as possible.

Step four: Assemble your layers. Begin with a layer of enchilada sauce (roughly ½ cup) at the bottom of your pan. This is important because having this liquid surrounding your squash layer will help the squash cook thoroughly. Then layer 1/3 of your squash, filling, and 1 cup of cheese. Repeat – squash, filling, and cheese. For the last layer, layer the remaining 1/3 of your squash and filling and then pour the last cup of enchilada sauce over your whole casserole. Lastly, cover with the last cup of cheese.  

Step five: Bake at 350 for 30 minutes covered with aluminum foil. Remove covering and bake for remaining 30 minutes until casserole is bubbling, cheese is melted and beginning to brown, and squash is fork tender. Let rest for at least 10 minutes before serving. Because the squash contains more moisture than tortillas would, the casserole does have a bit of liquid but this doesn’t impede the flavor or texture at all, especially when served over rice.

enchilada casserole with rice

Top as desired. Avocado slices or guacamole, sour cream, diced tomatoes, green onions, extra cheese. The more the merrier.

Serve and enjoy. This is one of those recipes that gets better with age and reheats perfectly, so we strongly encourage making enough butternut squash enchilada casserole for leftovers!

Butternut Squash Enchilada Casserole without Tortillas

Butternut Squash Enchilada Casserole without Tortillas

Yield: 8 servings
Prep Time: 1 hour
Cook Time: 1 hour
Total Time: 1 hour

This casserole is a delicious alternative to standard enchiladas, nourishing comfort food at its finest. It can easily be made keto friendly without beans or vegetarian by substituting extra veggies for the meat. It is a perfect way to use that extra shredded meat from a roast or whole chicken or leftover roasted vegetables. And you’ll find butternut squash to be the perfect, tasty substitute for tortillas.

Ingredients

  • Keep in mind this recipe is highly adaptable to what you have on hand, but here’s what we used…
  • 1 medium butternut squash (sliced 1/8” thick)
  • 3 cups shredded beef (or meat of choice)
  • 1 onion, diced
  • 1 pepper, diced
  • 3 cloves garlic
  • 4 cups black beans (or bean of choice)
  • 3 cups shredded cheese
  • 3 cups enchilada sauce
  • Spanish rice or cauliflower rice to serve casserole over (Optional)

Instructions

    1. Prepare three cups of your enchilada sauce. Here’s the recipe for our simple, from scratch version.
    2. Make your filling. In this recipe, I used a combination of shredded beef from a chuck roast, black beans, onions, garlic, and peppers. Dice and sauté your onions, garlic, and peppers. After your veggies are cooked, stir in beef and beans. Pour and incorporate 1.5 cups of enchilada sauce into the filling mixture. Set aside.
    3. Peel, seed, and slice your butternut squash into uniform slices (1/8”) either by hand or with a slicer. We use both the half circle and rainbow shaped portions – just adjust accordingly while laying on your pan so that it is fully covered as much as possible.
    4. Assemble your layers. Begin with a layer of enchilada sauce (roughly ½ cup) at the bottom of your pan. This is important because having this liquid surrounding your squash layer will help the squash cook thoroughly. Then layer 1/3 of your squash, filling, and 1 cup of cheese. Repeat – squash, filling, and cheese. For the last layer, layer the remaining 1/3 of your squash and filling and then pour the last cup of enchilada sauce over your whole casserole. Lastly, cover with the last cup of cheese.
    5. Bake at 350 for 30 minutes covered with aluminum foil. Remove covering and bake for remaining 30 minutes until casserole is bubbling, cheese is melted and beginning to brown, and squash is fork tender. Let rest for at least 10 minutes before serving. Because the squash contains more moisture than tortillas would, the casserole does have a bit of liquid but this doesn’t impede the flavor or texture at all, especially when served over rice.

    Top as desired. Avocado slices or guacamole, sour cream, diced tomatoes, green onions, extra cheese. The more the merrier.

 

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