Vegan Cheesy Baked Butternut Squash

March 25, 2021

Cheesy Baked Butternut Squash

This Vegan Cheesy Baked Butternut Squash dish will become one of your favorites. These Butternut squashes are filled with a hearty mix of brown rice, mushrooms, and homemade vegan cheesy Alfredo sauce. It is then twice-baked until the vegan cheese topping is melted and golden brown.
This recipe is by Nisha Vora at

Nisha Vora, the cookbook author and force behind the blog Rainbow Plant Life, is on a mission to help you master vegan cooking at home

Prep Time: 20 MINS

Cook Time: 1 HR 25 MINS

Total Time: 1 HR 45 MINS



Diet: Vegan

Keyword: butternut squash, nut-free, soy-free, vegan cheese

Serving size: 6


Butternut Squash:

  • 3 medium butternut squash (about 2 1/2 pounds or 1.1 kg each)
  • Olive oil or avocado oil (optional), or veggie broth for sauté
  • Kosher salt or sea salt (optional)

Farro Directions:

  • A few sprigs each of rosemary, sage, and thyme. I
  • 1 cup farro (semi-pearled or pearled*)
  • 2 ⅔ cups vegetable broth (or water)
  • 1 ½ teaspoons kosher salt, optional

Cheesy Alfredo Sauce:

  • 1/4 cup olive oil, or veggie broth
  • 1 large yellow onion, diced
  • 6 garlic cloves, minced
  • 4 tablespoons all-purpose flour
  • 1 (15- ounce) can (or 2 cups) “lite” coconut milk (can substitute unsweetened oat milk, cashew milk, or soy milk). I used Oat-ly Oat milk from Sprouts (also at Target).
  • 1 teaspoon kosher salt, optional
  • Freshly cracked black pepper to taste
  • 1/8 – 1/4 teaspoon nutmeg
  • 1/4 cup nutritional yeast
  • 1/2 cup grated vegan cheese, optional


  • 4 cups fresh baby spinach, julienned

Ingredients I added (optional):

  • 12 crimini brown mushrooms, chopped
  • 1/4 cup Panko bread crumbs
  • 2 green onions, chopped
  • 1 cup frozen peas
  • 1/2 cup Trader Joe’s Quick-Cook Organic Brown Basmati Rice
  • 1/2 cup Trader Joe’s Organic Tricolor Quinoa
  • 3 sprigs each of fresh rosemary, sage, & thyme (washed, Chiffonade, chopped)
  • 2 cups Oat-ly milk
  • 1/2 cup was Trader Joe’s Dairy-free Mozzarella Style Shreds Cashew Cheese
  • 1/4 cup So Dairy-free Coconutmilk yogurt
  • 1/8 teaspoon turmeric
  • 1/8 teaspoon ginger powder
  • 1 teaspoon garlic powder
  • 1 teaspoon onion powder
  • 1/4 teaspoon cinnamon

Brown Rice Directions for Stovetop:

  • Rinse rice well.
  • Bring 1 3/4 cup of water to a boil in a saucepan with a tight fitting lid.
  • Once the water is boiling, add 1 cup rice (add butter, salt, optional).
  • Cover and reduce heat to a simmer.
  • Cook for 15 minutes or until water is absorbed.
  • Once cooked, fluff the rice with a fork.
  • Measure 1/2 cup of cooked rice & combine with your cooked quinoa.

Quinoa Directions: Stovetop:

  • Place 1 cup quinoa and 2 cups water in a 1 1/2 quart saucepa, and bring to a boil.
  • Reduce to a simmer, cover, and cook until all the water is absorbed (for about 15 minutes).
  • When done, the grain appears soft and translucent, and the germ ring will be visible along the outside edge of the grain.
  • Measure 1/2 cup of cooked quinoa and combine with your cooked brown rice.


  • Add 2 parts water to 1 part quinoa in a microwave safe bowl.
  • Cover and heat on high for 4 minutes, then remove from heat and stir.
  • Heat again for an additional 2 minute.
  • Stir and let stand for 1 minute before eating.
  • Measure 1/2 cup of cooked quinoa and combine with your cooked brown rice.


  • Microwave each Butternut squash for 3 1/2 minutes. This will allow you to cut through it easily. Cut each squash lengthwise into two halves. Remove the seeds & center pulp, by carefully scooping it out with a spoon.
  • Bake the butternut squash. Preheat the oven to 400°F/205°C.

Place the butternut squash halves on a half sheet pan or large baking tray. Very lightly brush the squash flesh with the olive oil or avocado oil and lightly sprinkle with salt. You can bake the squash plain (without salt or oil), which is what I did. Bake the squash halves for 45-55 minutes or until fork-tender but not too soft, depending on the size of your squash. A 2 1/2 pound squash takes about 50 minutes.

Wash, peel, chop, & prepare your veggies. Wash, & scrub mushrooms tops with paper towels, & dry with clean paper towels. Peel & chop onion. Peel & mince the garlic. Julienne the spinach. Peel & chop the green onions. Measure out the rest of the ingredients and set aside.

Once the squash is done baking, and cool enough to handle, scoop out a good amount of the flesh but don’t scoop too deep or you might pierce the skin. I left about 1/4 inch flesh on each squash half. Transfer the squash flesh into a large bowl and mash pieces together with a fork. I used a blend of scooped out pulp and individual chunks of 1/4” of additional baked butternut squash (see photo above). Mix and set aside until ready to mix the stuffing. Leave the hollowed out squash halves on the baking sheet.

Cooked Tricolor Quinoa & Brown Rice

Make the farro: Using kitchen twine, tie together the stalks of fresh rosemary, sage, and thyme into a bundle. I cooked 1/2 cup Trader Joe’s Basmati Brown Rice, and 1/2 cup Trader Joe’s Tricolor quinoa. I cooked each individually and then combined the two (see photo above).

Reduce the oven temperature to 350°F/175°C, which is the temperature that you will use to bake the stuffed squash.

Cook the farro: Place the farro 2 2/3 cups broth or water, 1 1/2 teaspoons kosher salt, and the bundle of herbs in a medium saucepan. Bring to a boil over high heat, then reduce the heat to medium-low. Cover and simmer until the farro is tender but still chewy, about 25 minutes. Drain well. If you taste the farro before draining, it will taste very salty but it will lose some saltiness after you drain it. Fold the cooked farro into the reserved squash flesh.

Alfredo Sauce

Make the Cheesy Alfredo Sauce: Heat a large deep sauté pan or saucepan over medium heat and add the olive oil (if using), or use veggie broth. Once hot, add the onion and cook for 6-7 minutes until the onion is softened and lightly browned. Add the garlic and cook for 2 minutes, stirring frequently to prevent burning. Reduce the heat to medium-low and add the flour, whisking constantly for a minute until well incorporated and you have almost a paste-like texture. Gradually pour in the lite coconut milk or other plant-based milk in stages, whisking after each addition to prevent clumps, and then cook for 2 minutes until the sauce has thickened. Add the yogurt. Season with the 1 teaspoon kosher salt (if using), black pepper to taste, a pinch or two of nutmeg, and then add the nutritional yeast and shredded vegan cheese (if using). I added the fresh herbs during this step, and after adding the the milk.

Immersion blend the sauce until smooth.

Whisk the sauce until thick and the cheese is melted. Use an immersion blender to blend until the sauce is relatively smooth (or transfer to a stand blender). Add the frozen peas, and gently cook on low until peas are heated through. Taste the sauce for seasonings, adding more salt, pepper or nutmeg as desired.

Sauté the mushrooms.
Add the frozen peas.
Add the spinach.
Add the spices & mix until well incorporated.
Cover with a lid and steam.

Steam the spinach: heat a sauté pan over medium. Add the mushrooms, and sauté for 2 minutes. Add the frozen peas, spinach, green onions, all of the seasoning, and mix until well incorporated. Add a few tablespoons of water, then cover the pan, and allow the spinach to wilt and cook down and turn bright green. It should take just 2-5 minutes. Taste test it for seasonings, adding more salt, and pepper as desired.

Assemble the stuffed squash mixture.
Serve each half of the stuffed squash with a generous amount of the Cheesy Alfredo Sauce.

Assemble the stuffed squash mixture: In a large bowl, combine the squash flesh, spinach mixture (reserve some to top each squash), brown rice & quinoa, bread crumbs, and mix together until well incorporated (see photo above). Generously spoon the assembled squash mixture into the scooped out butternut squash halves. Then pour the cheesy alfredo sauce on top, completely covering the filling. Add a little freshly cracked black pepper on top, if desired. Bake at 350°F/175°C for 15-20 minutes until warmed through. Turn on the oven broiler and broil the stuffed squash for a minute or two until the cheesy alfredo sauce is browned in some spots.


  • Farro is not gluten-free, but is generally easier to digest than other gluten-containing grains. For a gluten-free option, substitute brown rice, millet, or quinoa.
  • Author uses kosher salt in most of her cooking, specifically the Diamond Crystal brand, which is the least salty salt by weight. If you use sea salt or table salt, cut this amount in half or your farro will be too salty.
  • For a gluten-free option, use a gluten-free all-purpose flour or rice flour in the roux.
  • Author used a mixture of Follow your Heart mozzarella and Chao Creamery slices and used a box grater (if you freeze the sliced cheese for a short period of time, it makes it easy to grate it).

How did you modify this recipe? Please share in the comments. Thank you for sharing!

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