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Spaghetti Squash Enchiladas

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This is a vegan spaghetti squash recipe you need to try!

These savory spaghetti squash enchiladas are filled with quinoa, caramelized onion, and pinto beans- making it a protein packed, healthy plant based meal.
These enchiladas are soy free, can be gluten free, can be oil free, and is made with whole foods!

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Squash and Bean Enchiladas are the Ultimate Healthy Cold Weather Food!

When the leaves start falling and it starts to get cold this is the perfect thing to bake up to warm the whole house. These spaghetti squash enchiladas are fantastic for meal prep- freeze up your leftovers to rebake for an easy meal!
(Or meal prep a pan of enchiladas for a future day!)
Growing up in Minnesota, casseroles like these enchiladas are a staple food!
It’s a family favorite that is simple and stores great- which is my it’s my favorite vegan spaghetti squash recipes!

These enchiladas are very simple to make- simply prepare your spaghetti squash by roasting it, season the beans, fry the onions, and season the quinoa and wrap them up in sauce to bake!

The sweet and shreddy spaghetti squash adds a fantastic textural element to these enchiladas.
The sweet yet mild flavor of the spaghetti squash is fantastic with onions and garlic. Then it is paired with some spicy pinto beans, crumbly lime quinoa, and caramelized onions.

enchiladas, salsa, and guacamole

Considerations When Preparing

This is one of those recipes that is fantastic to make at the beginning of the week because of the meal prep possibilities. This spaghetti squash recipe uses quinoa, and pinto beans- preparing these ingredients in advance will help you save time.

Try making a large batch of quinoa for not only this recipe, but as meal prep for the rest of the week. Having some plain precooked quinoa can speed up making more meals throughout the week. Think about the quick burrito, buddha bowl, and risotto possibilities!

The same can be said with preparing pinto beans!
Cooking pinto beans from dried is not only more sustainable- but it is much healthier since canned beans are loaded with salt and often have a plastic lined can. Before I invested in an instant pot I thrifted a crock pot and would use that to make dried beans. It is much more affordable to buy dried beans and cook them rather than buying a can.

To make beans in a slow cooker, simply add your dried beans and cover with a few inches of water over top overnight. When you cook your dried beans in a slow cooker over night you don’t need to presoak them!
If you have an instant pot cook your dried beans for 1 hour and they are ready to go- with no soaking. Then you’ll also be left with aquafaba- which is fantastic in soup broth and gravy. Don’t use pinto bean or black bean aquafaba for regular baking as it has a darker color that isn’t ideal in most recipes.

Roasting the spaghetti squash in advance is a great way meal prep for the week. If you have your spaghetti squash pre roasted before this recipe then it’s as simple as combing everything together into a burrito and covering it in sauce and plant based cheese.
If you have leftover spaghetti squash save it for adding to other burritos, add it to a pasta bake, or eat with seasoned with some garlic and plant based cheese.

Substitutions and Additions

Many of the ingredients can be swapped out to your preferences while still creating a perfect enchilada.
Instead of quinoa try using brown rice, black rice, or faro. If you are not a fan of pinto beans, try using great northern white beans, or classic black beans.

Consider adding some marinated TVP, your favorite plant based mince, or some homemade seitan. Instead of using premade plant based cheese, consider making a homemade queso!
If you love making food from scratch, consider trying out this red enchilada sauce recipe instead of using a can.

In the past I’ve roasted sweet potatoes in cumin and chipotle and added it to these enchiladas- it was fantastic. The same can be said with sweet corn- simply season it with some garlic and onion and it can make a delightful addition.
While the spaghetti squash isn’t necessary in these enchiladas- I strongly encourage you to try them. It’s one of my favorite vegan spaghetti squash recipes because the texture of it is awesome in enchiladas.

enchiladas cut open on a plate

Toppings for Serving

When serving the enchiladas consider drizzling over some more plant based queso, fresh salsa, and guacamole!
Sprinkle over some chives, cilantro, shredded lettuce or sprouts to make it more fresh!
Sure these enchiladas taste fantastic on their own- but adding fresh toppings to them really kicks them up a notch! Especially if you are health conscious and want to include more fresh veggies into your diet. This is vegan spaghetti squash recipe that can be both fresh, warming, and ultra comforting- while being healthy.

Meal Prep Ideas

Vegan Spaghetti Squash Casserole, or Enchiladas are a fantastic recipe to meal prep since they taste great reheated. Try making a double batch and freezing an entire pan of them for a future date. For best results freeze the assembled pan of enchiladas before you bake them. To bake them from frozen cover the pan while baking (with either a ceramic lid or tin foil) at 350 for 1 hr 30 minutes, then bake without any covering for an additional 30 minutes.

Consider meal prepping two enchiladas in a bread loaf pan- these pans are just the right size to fit two! Pop them in the freezer for an easy meal in the future. (Freezing a giant casserole dish might not be possible unless you have a big enough freezer, or have a chest freezer).

Try to eat the frozen enchiladas within 4-6 months of freezing so they don’t dry out too!

A enchilada on a plate

Spaghetti Squash Enchiladas

Garlicy shredded spaghetti squash encased in an enchilada with lime quinoa, spicy cumin pinto beans, caramelized onions, and plant based cheese.
These spaghetti squash enchiladas are the perfect combination of savory, sweet, and spicy while creating a hearty and warming plate.
Print Recipe
CourseVegan Recipes
Prep Time55 minutes
Cook Time45 minutes
Servings6 servings


  • 3 Cups Cooked Pinto Beans
  • 1/2 Whole Spaghetti Squash
  • 2 Large Sweet Onions
  • 1 can Red Enchilada Sauce
  • 1 Cup Quinoa
  • 1 1/2 Cup Water
  • 2-4 Cups Vegan Cheddar
  • 1 tbs Coconut Sugar*
  • 1/2 whole Lime
  • 6 large flour/corn tortillas

Spices For Pinto Beans

Spices for Spaghetti Squash


  • Preheat the oven to 400 F
  • Prepare your spaghetti squash by cutting it in half, removing the seeds and guts, and placing it on a baking sheet. Roast in the oven for 40-55 minutes (depending on size) until it is cooked through. Try pressing on the skin and if it leaves an indent it is ready. Scoop out the flesh Add all the spices for the spaghetti squash listed above- set aside
  • Prepare your quinoa by either cooking in an IP or over the stove. 1 cup quinoa to 1 1/4 cup water for 2 minutes, then let it natural release. Fluff with fork 1 cup quinoa to 1/2 cup water for 20 minutes over medium heat. Fluff with fork Squeeze half a life over it with a pinch of salt (or sprinkle over some Tajin seasoning)
  • Slice your onions into strips, then sauté over medium high heat, adding a pinch of salt and the coconut sugar to really get it to caramelize. Cook until dark brown and sticky- then set aside
  • In a large bowl add your 3 cups of precooked Pinto Beans and mix in all the spices for the pinto beans listed above
  • Reduce oven temperature to 350 F
  • Add half a can of enchilada sauce to your casserole dish Grab a tortilla and fill with a scoop of the spaghetti squash, the pinto beans, the onions, the quinoa, and a bit of vegan cheese. Wrap it up like a burrito and set inside the casserole dish Repeat until you’ve filled your casserole dish with the enchiladas Pour the remaining enchilada sauce over all the enchiladas, then sprinkle cheese over everything
  • Bake in the oven for 45-60 minutes- until it is golden brown on top
  • Serve with fresh salsa, guacamole, cilantro, shredded lettuce, and more plant based nacho cheese


  • 3 cups pinto beans is about 2 cans worth, consider making pinto beans from dried by cooking them in the IP for 1 hour- no soaking required! (This makes great meal prep for early in the week)
  • Don’t want quinoa? Try these enchiladas with your favorite rice!
  • Don’t have coconut sugar? Try using brown sugar or turbinado sugar with the onions. Another option is to use coconut amnios to help them caramelize
  • Nutrition

    Calories: 485kcal

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    By on November 19th, 2021

    About Jessica Flowers

    Jess Flowers is a multimedia specialist who creates vegan recipes using local and wild ingredients. Being plant based for over a decade, it is her mission to share delicious recipes that are made without animal products!

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