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Home » Vegetarian Main Dish Recipes

Butternut Squash Casserole

Modified: Jan 9, 2025. Published: Jan 9, 2025 by Lindsay Moe.

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Butternut squash casserole is a warm and comforting vegetarian dinner recipe that is full of protein and veggies!

Butternut squash quinoa casserole in a white baking dish next to a linen napkin, a small bowl of salt, and a small bowl of quinoa.
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  • Ingredients
  • How to make butternut squash casserole
  • FAQ
  • More butternut squash recipes
  • Recipe

Are you ready for the best butternut squash recipe?

I know, that seems nearly impossible when we've enjoyed other recipes like butternut squash and kale pizza and black bean and butternut squash quesadillas. But there's a new favorite in town!

Butternut squash casserole is inspired by my other quinoa casserole recipes, but uses my favorite winter vegetable alongside butter beans, pesto, and balsamic onions. It's cozy, comforting, and easy to make vegan.

Ingredients

  • Uncooked quinoa
  • Olive oil
  • Vegetable stock
  • Butternut squash
  • Onion
  • Garlic
  • Balsamic Vinegar
  • Canned diced tomatoes
  • Canned butter beans
  • Pesto
  • Coarse kosher salt and freshly ground black pepper
  • Italian cheese blend
  • Parmesan cheese
Ingredients used to make butternut squash quinoa casserole.

How to make butternut squash casserole

  1. Preheat the oven to 400ºF.
  2. Spread butternut squash cubes in a single layer on a large, rimmed baking sheet. Drizzle with 1 tablespoon olive oil (or more as needed) and use your hands to toss the cubes until completely coated. Season with salt and pepper to taste.
  3. Bake the squash for 35-45 minutes, or until soft and as caramelized as you prefer. After taking out the squash, reduce the oven temperature to 375ºF.
  4. Meanwhile, place the quinoa in a fine mesh strainer and rinse under cold water for 2 minutes.
  5. Heat 1 teaspoon of olive oil in a medium saucepan over medium heat. Once hot, add the quinoa and allow it to toast until the water has cooked off and they are beginning to pop around a little bit.
  6. Add the vegetable stock and bring to a boil. Cover, reduce the heat, and cook for 12 minutes or until the liquid has been absorbed. Remove from the heat, keep it covered, and allow it to rest while you prepare the other ingredients.
  7. Heat 1 tablespoon olive oil in a medium skillet over medium heat. Add the onions and cook, stirring frequently, for 7 minutes or until softened and just beginning to brown.
  8. Add the garlic and cook, stirring, for 1 more minute.
  9. Add the balsamic vinegar, stir until evaporated, and remove from the heat.
  10. In a large bowl, combine the squash, quinoa, onion mixture, diced tomatoes, butter beans, pesto, salt and pepper to taste, and 1 cup of the Italian cheese blend. Stir gently to combine.
  11. Spray a 9x13 baking dish with cooking spray and spread the mixture evenly to fill it.
  12. Bake the casserole for 30 minutes. Add the remaining cheeses to the top and bake for 10 minutes more.
A small bowl of butternut squash quinoa casserole, behind it is the full baking dish.

Top tips

Baking butternut squash cubes

Butternut squash is easy to cook when cut into cubes and roasted in the oven. Start by cutting away the top and bottom, then cut the neck off of the bulb. Cut off the skin with a large chef's knife or vegetable peeler.

I then cut the neck into ¾ inch rounds and cut those into cubes. If you have a big squash this may be enough and you don't need to fuss with the bulb, but if you want to make the most of your veggie, cut the bulb in half from top to bottom and scoop out the stringy seeds.

Remove the skin if you haven't already, then cut into ¾ inch strips and cut those into cubes. Toss the cubes with oil, salt, and pepper, and arrange in a single layer on a baking sheet. Roast in the oven at 425ºF, stirring every 10-15 minutes, until soft and caramelized.

Cubes of roasted butternut squash on a baking sheet.

How to cook quinoa

I have a whole post about how to cook quinoa, as well as how to cook quinoa in the instant pot. You could prepare it either way for this recipe, just note that I'm using a little more liquid than I normally do to help keep some moisture in the casserole.

The best way to reheat leftovers

All of my quinoa casserole recipes get even better as the flavors come together in the refrigerator. My favorite way to heat up these leftovers is to heat a skillet over medium heat, add a little oil, and then pan fry individual portions until hot and crispy. Pro tip - add a little extra cheese when reheating!

Onions with balsamic vinegar cooking in a pan.

How to store butternut squash and quinoa casserole

Keep leftovers covered in the refrigerator for up to 3 days. You can also freeze the entire casserole either baked or unbaked and covered tightly in plastic wrap for up to 3 months. 

Allow to thaw in the refrigerator overnight before baking, adding a few minutes to the bake time if it's still cold in the middle. If you froze it after baking, reheat in the oven or as individual portions in the microwave or in a skillet on the stove top.

Tips for customizing butternut squash casserole

  • Leave out the cheese and serve as a cold salad
  • Swap the pistachio pesto for a different variety
  • Instead of the balsamic onions, try caramelized onions
  • Use a different type of squash, such as acorn squash, pumpkin, or even sweet potato
Unbaked butternut squash quinoa casserole in a white baking dish.

FAQ

Can I use uncooked quinoa in this recipe?

If your quinoa is uncooked, I recommend cooking it before adding it to the rest of the ingredients. Otherwise it may come out too crunchy.

What kind of pesto should I use in butternut squash casserole?

I loved my pistachio pesto in this recipe, but I also tested it with regular basil pesto and it was fantastic as well. Changing up your pesto is a good way to try this recipe with different flavors. A sage pesto would also pair nicely with the squash.

What are butter beans?

Butter beans are a large white bean that has a creamy texture and mild flavor. I love adding them to soups, casseroles, and more.

They can be found in the bean aisle at the grocery store. You can use either large butter beans or baby butter beans in this recipe.

Is parmesan cheese vegetarian?

Real parmesan cheese is not vegetarian because it is made with animal rennet. If this is important to you, look for a parmesan cheese made with vegetable rennet.

A fork holding up a bite of butternut squash quinoa casserole.

More butternut squash recipes

  • Vegetarian Enchiladas with Butternut Squash
  • Butternut Squash Cake
  • Crispy Butternut Squash Ravioli
  • Pan Fried Butternut Squash Pasta
  • Butternut Squash Pizza with Kale
  • Butternut Squash Risotto with Kale
  • Butternut Squash Puree
  • Butternut Squash and Sage Pesto Grilled Cheese
  • Butternut Squash and Sage Pesto
  • Black Bean and Butternut Squash Quesadillas
  • Winter Salad with Butternut Squash
A small bowl of casserole and a small bowl of salt next to the casserole in a baking dish.

If you make this recipe, be sure to rate it, leave a comment, or tag #theliveinkitchen on Instagram!

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Recipe

A small bowl of butternut squash quinoa casserole.

Butternut Squash Quinoa Casserole

A vegetarian butternut squash quinoa casserole loaded with veggies, cheese, and protein. Flavored with pesto and balsamic onions.
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Prep Time: 20 minutes minutes
Cook Time: 1 hour hour 25 minutes minutes
Total Time: 1 hour hour 45 minutes minutes
Servings: 6
Calories: 488kcal
Author: Lindsay Moe
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Ingredients

  • 1 cup uncooked quinoa
  • 2-3 tablespoons olive oil, divided
  • 2 cups vegetable stock
  • 1 butternut squash, cut into ¾ inch cubes
  • 1 medium onion, diced
  • 2 cloves garlic, minced
  • 1 tablespoon balsamic vinegar
  • 15 ounces diced tomatoes, drained
  • 15 ounces butter beans, rinsed and drained
  • ¼ cup pesto
  • Coarse kosher salt and freshly ground black pepper
  • 2 cups Italian cheese blend, or mozzarella
  • ¼ cup freshly grated parmesan cheese

Instructions

  • Preheat the oven to 400ºF.
  • Spread butternut squash cubes in a single layer on a large, rimmed baking sheet. Drizzle with 1 tablespoon olive oil (or more as needed) and use your hands to toss the cubes until completely coated. Season with salt and pepper to taste.
  • Bake the squash for 35-45 minutes, or until soft and as caramelized as you prefer. After taking out the squash, reduce the oven temperature to 375ºF.
  • Meanwhile, place the quinoa in a fine mesh strainer and rinse under cold water for 2 minutes.
  • Heat 1 teaspoon of olive oil in a medium saucepan over medium heat. Once hot, add the quinoa and allow it to toast until the water has cooked off and they are begging to pop around a little bit.
  • Add the vegetable stock and bring to a boil. Cover, reduce the heat, and cook for 12 minutes or until the liquid has been absorbed. Remove from the heat, keep it covered, and allow it to rest while you prepare the other ingredients.
  • Heat 1 tablespoon olive oil in a medium skillet over medium heat. Add the onions and cook, stirring frequently, for 7 minutes or until softened and just beginning to brown.
  • Add the garlic and cook, stirring, for 1 more minute.
  • Add the balsamic vinegar, stir until evaporated, and remove from the heat.
  • In a large bowl, combine the squash, quinoa, onion mixture, diced tomatoes, butter beans, pesto, salt and pepper to taste, and 1 cup of the Italian cheese blend. Stir gently to combine.
  • Spray a 9x13 baking dish with cooking spray and spread the mixture evenly to fill it.
  • Bake the casserole for 30 minutes. Add the remaining cheeses to the top and bake for 10 minutes more.

Notes

 

Tips for customizing butternut squash casserole

  • Leave out the cheese and serve as a cold salad
  • Swap the pistachio pesto for a different variety
  • Instead of the balsamic onions, try caramelized onions
  • Use a different type of squash, such as acorn squash, pumpkin, or even sweet potato

Nutrition

Calories: 488kcal | Carbohydrates: 57g | Protein: 23g | Fat: 21g | Saturated Fat: 4g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 4g | Cholesterol: 12mg | Sodium: 1052mg | Potassium: 1134mg | Fiber: 11g | Sugar: 9g | Vitamin A: 13786IU | Vitamin C: 35mg | Calcium: 243mg | Iron: 5mg
Tried this recipe?Mention @theliveinkitchen or tag #theliveinkitchen!

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lindsay moe in a kitchen with glasses on shelves behind her

Hi, I'm Lindsay! I've been creating easily customizable vegetarian recipes since 2011. I love the outdoors, brownies, and brand new books. I live and work in La Crosse, Wisconsin and founded Wild Flour Media to expand on my love for food photography and videography to my community and beyond.

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