Butternut Squash Quinoa Casserole

4.69 from 74 votes

Posted December 28, 2020 (last updated November 13, 2023) by Wendy Polisi

This post may contain affiliate links. All opinions are my own.

Butternut Squash Quinoa Casserole is one you don't want to miss! This recipe works just as well as a weeknight standby as it does on your holiday table. Have fun with it and adapt it to suit your needs - adding in cooked chicken or tempeh is an excellent way to up the protein factor, or you can add sauteed spinach for more vegetables.

Photo of Butternut Squash Casserole with Quinoa in a casserole dish garnished with sage against a white background.

This time of year, I want to eat meals that leave me feeling my best. The challenge is that the weather has me craving comfort food.

Today’s casserole is my favorite kind of vegetarian main dish. Flavor packed, hearty, and cheesy.

It takes butternut squash casserole to a whole new level!

To me, it is the perfect example of comfort food that you don’t have to feel guilty about enjoying.

Did you know that just one cup of butternut squash has 160 percent of your recommended amount of vitamin A?

Vitamin A is important to keep your immune system, skin and eyes in good shape. It also happens to be really good for your gut. It is needed to help the body assimilate nutrients.

You can read more about the health benefits of butternut squash here.

Ingredients

Butternut Squash - I like to buy a whole butternut squash and peel and dice it, but you can buy pre-chopped butternut squash in the produce section if you are short on time. Frozen chopped squash also works in a pinch!
Olive Oil - Any oil you choose, such as avocado oil, will work.
Shallots - If you don't have shallots, ½ cup of chopped red onion would be a good substitute.
Sage - I encourage you to stick with fresh sage here - dried just doesn't compare. If dried is your only option, I would recommend ½ teaspoon.
Garlic - I know that six cloves of garlic seem like a lot, but it really adds to the dish's flavor. If you don't care for garlic, feel free to reduce the amount used.
Quinoa - You will need one cup of uncooked quinoa for this recipe. I like white quinoa as I find the texture of red quinoa a bit too firm for casseroles. You decide what works for you.
Broth - I prefer to make my broth homemade using vegetable scrapes because I feel that the flavor is superior to any commercially available broths. Do whatever works for you!
Salt and Pepper - My preference is for finely ground pink Himalayan sea salt and fresh ground black pepper
Cayenne Pepper - This adds a subtle kick of heat, which I don't find to be at all overpowering. If heat is not your thing, feel free to leave it off.
Eggs - I use large eggs. If you are vegan or allergic to eggs, just leave them off.
Milk - Any kind of unsweetened milk will work in this recipe.
Cheese - If you are not vegan, Gruyere cheese is exceptional here. If you don't have it, use whatever cheese you have on hand. For a vegan option, either use gluten-free breadcrumbs or vegan cheese.

How to Make Vegetarian Quinoa Butternut Squash Casserole

This is a visual walk through for those who like to see the steps. For the full recipe, see the recipe card below.

Photo of butternut squash, raw quinoa, onion, garlic, seasonings, gage, eggs, olive oil and broth in prep bowls.

Step 1: Gather Your Ingredients

You will need diced butternut squash, olive oil, minced shallots, chopped sage, garlic, quinoa, broth, salt, pepper, cayenne pepper, eggs, milk, and cheese.

Cubed Butternut Squash in a roasting pan.

Step 2: Roast the Squash

Preheat the oven to 350 degrees. Prepare a baking sheet by spraying with oil. You can line it with parchment if you choose. Add the squash and season with salt and pepper. Roast for 15 minutes.

Onion and garlic being sauteed in a sauce pan with a spoon in it sitting on a white background.

Step 3: Cook shallots, sage and garlic.

When the squash has been in for about 8 minutes, heat oil in a saucepan over medium heat. Add shallots and sage and cook for 8 minutes. Add in garlic and cook for another 30 seconds.

Quinoa and Butternut Squash being added to the pan to cook.

Step 4: Add Quinoa and Butternut Squash

Add the quinoa and butternut squash to the pan with the shallots and cook for another minute.

Liquid added to the pot to cook the quinoa and butternut squash.

Step 5: Add Broth and Seasonings.

Add in the broth, salt, pepper and cayenne pepper. Bring the mixture to a simmer, and then reduce the heat to low. Cover and cook for about 25 minutes, until the liquid is absorbed. Your quinoa should be cooked at this point.

Butternut Squash Casserole in a baking dish with the egg mixture being added to the pan.

Step 6: Transfer to a Baking Dish and add Eggs and Milk.

Transfer the butternut squash mixture to a baking dish. Whisk together the eggs and milk and pour the liquid over the quinoa and butternut squash mixture.

Butternut Squash Casserole with Quinoa ready to go in the oven.

Step 7: Top with Cheese and Bake

Top with grated cheese and bake. If desired, broil for 2 minutes to brown the top.

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Frequently Asked Questions

Can You Make This Dish Ahead of Time?

Yes! One of the best ways to prep for the holidays or the busy work week is to prepare casseroles ahead of time. This quinoa casserole may be made up to two days before baking. Allow to sit at room temperature for at least 30 minutes before putting in the oven. Alternatively, place in a cold oven and allow the pan to warm as your oven preheats.

Can You Freeze It?

Yes! This casserole may be frozen before or after baking. To freeze, allow to cool completely and then wrap tightly. Prior to cooking or reheating, it is best to let the casserole thaw in the refrigerator.

How do you store butternut squash?

Butternut squash can safely be stored at room temperature in a dark space for up to a month.

Variations for Butternut Squash Quinoa Casserole

For add a nutritional punch, add in 8 ounces of sautéed spinach or kale before baking.
For a more traditional “holiday feel” Butternut Squash Casserole, omit the cheese. Instead mix ¼ cup melted butter, ¼ cup brown sugar, ½ cup toasted pecans, ½ cup oats and ¼ cup flour. Sprinkle on top of the casserole before baking.
Saute 6 ounces chopped mushrooms and add to the mixture prior to baking.

Make it Easier

If you are pressed for time you can buy pre-cut butternut squash in the produce section. You can also find it in the freezer section. While this is a time saving option, you should expect package squash to have an inferior texture and taste to that which you peel and cut yourself. You decide if the trade-off is worth it!
Buy shredded cheese. Again, I do find there is a bit of a trade off in flavor, but this is a great option for when you are pressed with time.

Tips for Making Butternut Squash Casserole Recipes

This makes a great side dish or vegetarian main course. To make this vegan, omit the eggs and add in an additional ¼ cup of nut milk. If you would prefer to skip the vegan cheese, breadcrumbs work great here too.
I recommend using the best quality cheese you can here. A good Gruyere really adds a lot of flavor!

Photo of butternut squash quinoa in a blue casserole dish on a white napkin.

Buying Butternut Squash

The exterior of butternut squash should be very hard and free from any soft spots. It should feel heavy for its size.

If You Like This Recipe You May Also Like:

Everyone loves this Healthy Butternut Squash Soup! It is like a hug in a bowl.
Quinoa & Butternut Squash with Maple Tahini Dressing is a hearty salad that is perfect for fall.
Butternut Squash Quinoa Risotto is a wholesome twist on a classic! Easy to make and full of flavor, this is a recipe you will turn to again and again.
When you are looking for a hearty plant-based meal, this Vegan Black Bean Soup is perfection.

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4.69 from 74 votes