Vegetarian Butternut Squash Quinoa Casserole

Modified: Jan 13, 2026 · Published: Dec 28, 2020 by Wendy Polisi · This post may contain affiliate links ·

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 a casserole dish with butternut squash quinoa casserole.

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!

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

Let's Talk Ingredients

I usually start with a whole butternut squash, but if you’re short on time, pre-chopped or even frozen squash works just fine. Shallots are my favorite here, but I’ve made this with red onion and it was a good substitution.

Fresh sage gives the best flavor, so use that if you can. Dried works in a pinch (about ½ teaspoon). Six cloves of garlic might sound like a lot, but it really makes the dish; just scale back if you prefer a milder flavor.

I’ve made this with both red and white quinoa, and have a strong preference for white. Red is great in salad, but the texture is too firm for casseroles, in my opinion.

If you are vegan, just omit the eggs and use unsweetened milk. You can top with breadcrumbs or your favorite vegan cheese.

How to Make Vegetarian Butternut Squash Casserole with Quinoa

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

Cubed Butternut Squash in a roasting pan. — **Step 1: Roast the Squash**

Preheat the oven to 350 degrees. Prepare a casserole dish 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 for a Butternut Squash Casserole. — **Step 2: 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.

Wendy's Tips and Tricks

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 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 a slightly inferior texture and taste to that which you peel and cut yourself. You decide if the trade-off is worth it!
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.
If you want to make this for meal prep, leftovers will keep in an airtight container for up to three days. This recipe freezes well for up to a month.
Feel free to add other veggies - sauteed spinach, corn, broccoli, tomatoes, and bell pepper are all great options.

Variations for Butternut Squash Quinoa Casserole

Add in 8 ounces of sautéed spinach, kale or mushrooms 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.

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

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Square close up photo of butternut squash quinoa casserole in a casserole dish.

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4.74 from 89 votes