Cheesy Baked Butternut Squash (Vegan)

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If you think being vegan means missing out on Thanksgiving, these Cheesy Baked Butternut Squash will change your mind! Butternut squash is filled with hearty grains and a cheesy Alfredo sauce and then baked again until melty and golden brown. Serve as a hearty main dish for the holidays!
Prep Time: 20 mins
Cook Time: 1 hr 25 mins
Total Time: 1 hr 45 mins
5 from 10 votes

With Thanksgiving less than a week away, it’s time to crank my recipe delivery into full gear. In this last week, I’ve already shared the secrets to the best vegan mashed potatoes, a fun and unique stuffing that can double as your holiday table centerpiece, and an elegant spin on pumpkin pie. Oh, and also a roundup of 30 vegan recipes you can make for Thanksgiving.

So now it’s time for Thanksgiving main dish ideas! Of course, you can buy a tofurkey or one of many new vegan turkey alternatives on the market. I am so happy these cruelty-free alternatives exist, but TBH, I was never a fan of turkey. In all my years of making Thanksgiving for my family (I started at 15), I never cooked a turkey (my parents are vegetarian and appreciated that).

And when friends would make a turkey, I barely touched it. It was almost always dry and lacking in flavor, and even before I became vegan, I never understood this national obsession with turkey for one day only. A tradition that sadly results in millions of turkeys being killed despite the fact that most people don’t even enjoy eating turkey!

So, I’ve always been more into the side dishes. And while I would happily eat a plate full of side dishes any year, I did want to offer a few main dish options for vegans and vegetarians (or aspiring vegans or vegetarians) who want to feel like they’re also able to enjoy a main dish at Thanksgiving.

Hence these Cheesy Baked Butternut Squash! This recipe is hearty, indulgent, and finger lickin’ good, so you definitely won’t feel like you’re missing out at Thanksgiving! And for another brand new main dish idea, check out my Creamy Lentil Winter Bake!

For the recipe video and visual instructions, be sure to check out the Youtube video!

While this dish is rich and tastes indulgent, it’s still made with wholesome ingredients. Which means you’ll not only be able to get your non-vegan guests to happily enjoy it, but you’ll also be able to save room for dessert without having to put on your stretchy pants.

And while I like to present this Cheesy Baked Butternut Squash as a main course, you could also slice each squash half into two or three pieces and serve it as a side dish.

Now let’s talk about the ingredients and components in this Cheesy Baked Butternut Squash!

Butternut Squash

  • This recipe starts off by cutting butternut squash in half, lengthwise. You need a large, sharp knife to do this. It helps to sharpen your knife in advance (if you have a knife sharpener at home). To slice in half, I recommend first slicing off the stem on top and then slicing off a thin layer on one side of the squash so it can stay flat on the board without wobbling around. Then apply a slow, steady rocking motion throughout the squash.

    • If you’re having trouble with slicing the squash and feel its too tough, place your squash in the microwave for 1-2 minutes to soften it up. Still too tough? Add another minute.

  • Then you’ll bake the butternut squash halves in the oven until they’re fork-tender but not too soft. You can bake them plain, but I like to lightly brush the flesh with a bit of olive oil or avocado oil – I find that the squash retains more moisture this way and is less likely to dry out. And I also like to sprinkle the flesh with a bit of salt. There is salt in the filling but if you get a piece of the squash without the filling, it’s not going to have much flavor.

  • As I mention in the video, I use 3 medium-sized butternut squash that each weigh about 2 1/2 pounds (roughly 40 ounces or 1.1 kilograms). These take about 50 minutes to bake at 400°F/205°C, but if you use squash that are bigger (or smaller), you’ll need to bake them for a longer (or shorter) time.

  • Once the squash halves are done baking and cool enough to handle, scoop out the seeds in the cavity. Then scrape out a good amount of the flesh, leaving a bit of flesh around the border. Don’t scoop too deeply or you might pierce the skin of the squash. Leave the squash halves on the baking tray that you baked them on and transfer the scooped out flesh to a large bowl.

Farro Filling

  • Farro is one of my favorite grains (it’s probably a tie with millet). It has a chewy texture and nutty bite that are so irresistible and make it taste hearty and even indulgent.

  • However, farro is not gluten-free, so if you are gluten-free, I recommend substituting it with brown rice, quinoa, or millet. You will need to alter the cook times and liquid ratio if you use a different grain.

    • While farro does contain gluten, it is an ancient grain that is less processed than typical grains, and many people who have a mild gluten intolerance report being able to digest it without any issue.

  • To infuse flavor into the farro, I cook it in vegetable broth instead of water, and I season it with kosher salt and a trio of fresh herbs. These herbs—rosemary, sage, and thyme—go particularly well with winter squash, but you could easily substitute them to your liking or depending on what you have on hand. For instance, you can use just thyme and sage, or you can use rosemary and oregano.

  • I do want to mention that I use kosher salt in most of my 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. And if you taste your farro before draining (e.g., to test whether it’s done), it will taste quite salty. But don’t worry, once you drain it, some of the salt will drain off.

  • Be sure to test it at the 25 minute mark, as indicated in the recipe; otherwise, you risk overcooking it past the al dente point. It will be fine, but it won’t have as much chewy bite.

  • Once the farro is cooked, you’ll fold it into the reserved butternut squash flesh that you scraped out of the squash halves.

Cheesy Baked Butternut Squash (Vegan)

Cheesy Garlic Alfredo Sauce

  • I absolutely love my garlic alfredo sauce – it is the most flavorful and delicious alfredo sauce but 100% vegan and dairy-free. You can find it in some of my other recipes, such as my Pumpkin Ricotta Stuffed Shells or my Pumpkin Alfredo Pasta.

  • Here, I use that same sauce but I make it cheesy! Because it’s the holidays and I want some to be able to serve and enjoy some decadent food :)

  • The basic ingredients include olive oil, onions, garlic, flour, lite coconut milk, salt, pepper and nutmeg. And to make it cheesy, I add nutritional yeast and shredded vegan cheese.

  • Regarding substitution for this sauce:

    • If you are gluten-free, you can use gluten-free all-purpose flour or rice flour in the roux.

    • I like to use “lite” coconut milk from a can, but you can easily substitute another unsweetened plant-based milk. But be sure to choose a relatively thick variety such oat milk, cashew milk, or soy milk. Almond milk is too thin.

    • If you can’t find vegan cheese where you live or don’t want to use or don’t eat processed foods, feel free to omit it. This recipe will still be very delicious as is!

Spinach

  • Not much to say here, but since this is a creamy rich dish, I like to add a bit of baby spinach to the filling for balance.

  • I simply sauté/steam the baby spinach in a pan with a bit of water until it’s wilted. You could even steam it in the microwave to keep things really simple.

  • Or for a heartier green, you can use sautéed or steamed kale instead!

Now here are some tips on putting this Cheesy Baked Butternut Squash together!

Once you have all the main components ready—baked butternut squash halves, cooked farro, cheesy garlic alfredo sauce, cooked spinach—it’s time to assemble them.

  • First, mix together the cooked farro and the scooped out butternut squash flesh. You can add a pinch of salt or pepper to this filling if you’d like.

  • Fill each of the six squash cavities with this farro mixture, filling almost up the top.

  • Divide the cooked spinach amongst each squash.

  • Then ladle a generous amount of the cheesy garlic alfredo sauce on to each squash half, completely covering the filling with the sauce. Add a final crack of black pepper on top if desired.

  • Bake the stuffed squash at 350°F/175°C for 15-20 minutes until warmed through, and then turn on your broiler. Allow the squash to broil for a few minutes, or until the cheesy sauce is a bit browned in some spots.

In terms of maximizing efficiency and time when making this dish, you have two options.

  • Option 1: Make some of the components ahead of time. You can make the cheesy garlic alfredo sauce and farro filling ahead of time. Then, on the day of serving, bake your butternut squash halves, quickly cook the spinach, and then assemble the stuffed squash halves and return them to the oven to finish the dish.

  • Option 2: Make everything on the day off. This is what I do in the video. I start by pre-baking the butternut squash. As soon as I put them in the oven, I start on the farro filling. And while that’s cooking (it doesn’t need any babysitting or stirring), I prep the ingredients for the cheesy garlic alfredo sauce and start cooking it, along with steaming the spinach. By the time the squash is done baking and cool enough to handle, all the components should be ready. Then I stuff and assemble the squash and return them to the oven.

That’s about all you need to know about this delicious vegan Cheesy Baked Butternut Squash! I hope you give this recipe a try at Thanksgiving (or another holiday) this year! If you make it, be sure to leave a comment below with your feedback and tag me on Instagram with your recreations!

Cheesy Baked Butternut Squash (Vegan)

5 from 10 votes
If you think being vegan means missing out on Thanksgiving, these Cheesy Baked Butternut Squash will change your mind! Butternut squash is filled with hearty grains and a cheesy Alfredo sauce and then baked again until melty and golden brown. Serve as a hearty main dish for the holidays!
Prep Time: 20 mins
Cook Time: 1 hr 25 mins
Total Time: 1 hr 45 mins
Course: Dinner, Side Dish
Cuisine: American
Diet Vegan
Keyword: butternut squash, nut-free, soy-free, vegan cheese
Serving size: 6

Ingredients

Butternut Squash

  • 3 medium butternut squash (about 2 1/2 pounds or 1.1 kg each)
  • Olive oil or avocado oil (optional)
  • Kosher salt or sea salt (optional but recommended)

Farro

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

Cheesy Alfredo Sauce

  • 1/4 cup olive oil
  • 1 large yellow onion, diced
  • 6 garlic cloves, minced
  • 4 tablespoons all-purpose flour***
  • 1 (15- ounce) can “lite” coconut milk (can substitute unsweetened oat milk, cashew milk, or soy milk)
  • 1 teaspoon kosher salt
  • Freshly cracked black pepper to taste
  • 1/8 - 1/4 teaspoon nutmeg
  • 1/4 cup nutritional yeast
  • 1/2 cup grated vegan cheese (optional)****

Spinach

  • 4 cups baby spinach

Instructions

  • Bake the butternut squash. Preheat the oven to 400°F/205°C. Slice each butternut squash in half, lengthwise. To see how I slice it in half, see the video at 00:40. If your squash is too tough to slice, put it in the microwave for 2 minutes to soften.
  • 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 roast the squash plain (without salt or oil, but it bakes better and adds more flavor with the oil and salt). 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.
  • Once the squash is done baking and cool enough to handle, use a spoon to scoop out the seeds and sticky gunk. Then scoop out a good amount of the flesh but don’t scoop too deep or you might pierce the skin. Transfer the squash flesh in a large bowl and set aside. Leave the hollowed out squash halves on the baking sheet.
  • Reduce the oven temperature to 350°F/175°C or turn off until ready to assemble the stuffed squash.
  • While the squash is baking, make the farro. Using kitchen twine, tie together the stalks of fresh rosemary, sage, and thyme into a bundle. To see how I do this, see the video at 01:45.
  • 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.
  • While the farro is cooking and squash is baking, make the Cheesy Alfredo Sauce. Heat a large deep sauté pan or saucepan over medium heat and add the olive oil. 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. Season with the 1 teaspoon kosher salt, black pepper to taste, a pinch or two of nutmeg, and then add the nutritional yeast and shredded vegan cheese (if using).
  • 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). Taste the sauce for seasonings, adding more salt, pepper or nutmeg as desired.
  • Steam the spinach: heat a sauté pan over medium. Add the baby spinach and gently toss and turn with tongs. 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 1-2 minutes.
  • Assemble the stuffed squash. Spoon the squash and farro mixture into the scooped out butternut squash halves. Top each squash with some of the cooked spinach. 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.

Notes

* 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.
** I use kosher salt in most of my 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.
**** I 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). You can also use pre-shredded vegan cheese.

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22 comments on Cheesy Baked Butternut Squash (Vegan)

  1. Iralyn

    5 stars
    A very yummy and unique meal! There are a lot of steps and it takes a lot of cooking time overall (our squash took 1-1.25 hrs to bc tender), but everything is super easy and you can space things out as needed. We roasted the squash and let it sit while we did other things, then made the fillings and let those sit, then combined and baked when we were ready to eat. Husband said he could eat this every day! I agree with another review, don’t be short with the spices and salt! Salting and tasting every step of the way always helps from my experience.

  2. Lindsay

    5 stars
    Really delicious and comforting. To be honest, I could have just eaten a bowlful of that sauce and died happy 😃

    1. Lindsay

      Forgot to say, I used buckwheat as a gluten-free alternative and it worked really well.

  3. Shuvya

    5 stars
    This was really good although the flavors were a bit mellow for my spice-crazed family. The farrow and butternut squash can be a bit bland so make sure to not shy away from the seasonings!

  4. Lauren

    5 stars
    Worth the effort! Omg the cheesy sauce is so good! Gonna incorporate your sauce recipe into my chickn alfredo! Thank you!

  5. Kelsey

    5 stars
    Really enjoyed this recipe. Enjoyed it as part of our Christmas lunch. The cheese sauce was delicious and the dish looked beautiful on the table.

  6. Betsy

    Amazing!

  7. Dolores Walker

    Made last night. The best ever. Use brown rice

  8. Katie

    All of your recipes are amazing, I can’t wait to try out the butternut squash. For the gluten free option, do I still cook it with the rosemary, sage, and thyme? Thanks!

    1. Nisha Vora

      Hi Katie, that’s so nice to hear :) Thank you for the lovely feedback! Yes, I would cook whatever grain you are making with the fresh herbs – adds a lot of flavor :) Hope you enjoy it!

  9. Lisa

    Great recipe. I ended up just placing everything in little ramekins instead of back in hollowed our squash.

    1. Nisha Vora

      Hi Lisa, I’m happy to hear you enjoyed the recipe. I like the idea of individual sized ramekins for serving :)

  10. christina

    Hey Nisha!
    I just came here to review this recipe. It’s SO good, really! I made it as the only vegan dish for a traditional Thanksgiving, and everyone loved it. I was honestly skeptical because I’ve never had stuffed butternut squash and vegan cheese (even as a vegan) stresses me out!- but it turned out delicious. Thank you so much for your wonderful recipes. I love coming here for your fancy ones and your casual ones are just as unique and decadent tasting, and every one I’ve ever made has never disappointed.

    1. Nisha Vora

      Hi Christina, I am so happy to hear that you (and everyone else) loved the recipe! Haha yes, vegan cheese can be stressful, I totally get it. I am so happy you love my fancy and casual recipes and so nice to hear that you’ve loved them all :) Thank you!

  11. Bianca Zapatka

    I totally love any kind of baked pumpkin or squash! Especially, when you add a delicious filling that is cheesy, and vegan! So this stuffed squash recipe is just perfect for Christmas or any other day! Love your photos, Nisha! Happy Thanksgiving! 😘❤️

    1. Nisha Vora

      Thank you dear Bianca! The filling is so comforting :) Definitely a good idea for Christmas or any special occasion.

  12. Sharon

    Hi Nisha! This will be hitting our thanksgiving table today. Happy Thanksgiving to you and your family!! :) Sharon

    1. Nisha Vora

      Ooh I can’t wait to see! Hope you and your family enjoyed this!

  13. Steph GP

    I am making this, along with the lentil dish (subbing cauliflower for rutabaga)fc, for Thanksgiving. I’m looking forward to it!

    1. Nisha Vora

      That sounds wonderful, Steph! So happy to hear that and I hope you enjoyed the dishes and had a great Thanksgiving!

  14. Hannah | Two Spoons

    Nisha this butternut squash looks so tasty! Can’t believe how cheesy it looks. And you’re right, nobody would ever know it’s vegan (unless you told them, haha). Perfect for Thanksgiving! Hope you have a great one and thanks for sharing this recipe!!

    1. Nisha Vora

      Thank you, Hannah! Haha yes that’s right :) Thank you for stopping by and for the wishes!

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