As an Amazon Associate I earn from qualifying purchases.

This vegan butternut squash mac and cheese is creamy, comforting, wholesome, and requires just 9 ingredients (plus salt & pepper)! Make this vegan mac and cheese without cashews, processed ingredients, gluten-free optional, and get ready to indulge!

completed Butternut Squash Mac n’ Cheese in a skillet against a white background

Creamy, Cheesy, Butternut Squash Mac and Cheese

Whether you’ve been vegan for years and years or are brand new to it, comfort food classic mac and cheese is for everyone! We’ve already shared recipes for baked potato mac, a simple cheesy mac, and a veggie macaroni cheese bake; now it’s the turn of this healthy vegan butternut squash mac and cheese. It’s creamy, cozy, comforting, and so delicious that you’d hardly guess that it’s healthy!

What’s not to love? It’s made with inexpensive pantry staples (which means a vegan mac and cheese without cashews, yay!), allows you to sneak in extra veggies into a meal (and is child-approved!), is made with 100% whole food ingredients (nothing processed!), and can be made ahead and/or frozen for later! Plus, the combination of butternut squash, onion, nutritional yeast, and Dijon mustard makes for the most subtly sweet, savory, ‘cheesy’, super creamy butternut squash pasta sauce!

We’ve also included a bonus section on how to cook butternut squash (including boiled, steamed, baked, and air-fried butternut squash), so you can use whichever method works best for you. And, even better, this healthy vegan mac and cheese is incredibly flexible. So keep reading for ingredient substitutions, variations, and optional add-ins!

You can also enjoy this creamy squash as part of this butternut squash curry, creamy curried butternut squash lentil soup, butternut squash burrito, or Thai butternut soup!

The Ingredients:

  • Butternut squash: You need around half of a large butternut squash (2 cups). Here’s an easy hack to roasting Butternut Squash with ease!
  • Vegetable broth: Use homemade or store-bought. Use reduced-sodium vegetable stock if preferred.
  • Nutritional yeast: This provides the ‘cheesy’, umami flavor. Adjust to taste.
  • Onion: Use white onion rather than red.
  • Dijon mustard: Will add slight depth and tang to the sauce.
  • Vegan butter: Use unsalted vegan butter to create a roux for the butternut squash vegan cheese sauce.
  • All-purpose flour: For a gluten-free option, you could use rice flour, an AP gluten-free flour, or even cornstarch (though you wouldn’t make a roux with the latter. Instead, add a cornstarch slurry to the blended sauce and simmer until thickened).
  • Plant-based milk: Use unsweetened milk (oat milk, soy milk, cashew milk, etc.)
  • Pasta: Any short-shaped pasta will work, including macaroni, shells, rotini, penne, etc. Use gluten-free pasta if preferred.
  • Salt & Pepper
  • Optional seasonings: Garlic powder, onion powder, and/or red pepper flakes (or a pinch of chili/cayenne powder) are all optional seasonings. Start with ½ tsp and increase to taste.

ingredients for Butternut Squash Mac n’ Cheese measured out against a white surface

Optional add-ins & Recipe Variations

Low-Budget Add-ins

  • Lemon juice: A squeeze of lemon juice helps to add a slight tang (found in dairy-based cheese) and boost the flavor in a simple way. Alternatively, use apple cider vinegar.
  • Garlic: We recommend using roasted garlic for the best flavor, but raw/sauteed will work.
  • Breadcrumbs: Regular, panko, or gluten-free to top the vegan butternut squash mac n cheese and broil.
  • Sage: Use crispy sage (in a bit of vegan butter) to garnish.
  • Herbs: Rosemary, thyme, and sage pair wonderfully with butternut squash. Here’s an article on how best to store herbs to keep them fresh!
  • Other vegetables (for the sauce): Cooked carrot, potato, and parsnip can all be used to make ‘hidden veggie mac and cheese’ (add about ½ cup) for extra nutrients. Add 1 or 2 of any (or a combination) when cooking the squash.
  • Vegetables (to mix in): Add peas, corn, spinach, kale, leek, sauteed mushrooms, broccoli, cauliflower, zucchini, etc.
  • Smoked paprika: The subtle smokiness works amazingly to enhance vegan ‘cheesy’ recipes.
  • Nutmeg: Just a pinch adds depth to the sauce in a way where you can’t taste it there, but it definitely adds ‘something.’

A little something extra

  • Nuts/seeds: Lightly toasted walnuts, almonds, pistachios, pine nuts, pepitas, or sunflower seeds can be used to garnish the butternut vegan mac and cheese for healthy fats & crunch.
  • Soaked cashews: You can definitely have a delicious vegan mac and cheese without cashews, but add some if you want a super creamy butternut squash vegan cheese sauce.
  • Protein: Boost the protein amount with the addition of crispy chickpeas, marinated tofu (like these sweet and salty tofu bites), or your favorite cooked meat alternative (like vegan chorizo, sausage, bacon, etc.).
  • White miso: Add ½-1 tbsp white miso to the sauce for extra umami and depth for a more ‘cheddar-like’ flavor.
  • Vegan cheese: To enhance the cheesy flavor, feel free to add your favorite vegan melty cheese. Smoky cheese works particularly well with butternut squash mac n cheese.

completed Butternut Squash Mac n’ Cheese in a skillet with a serving separated into a small white bowl on the side against a white background

How to Cook Butternut Squash?

How to cut butternut squash

Depending on which cooking method you use, you can cook the squash in halves OR 1-inch cubes.

Halved: First, wash the squash and pat it dry. Then, slice the top and bottom off the squash and use a long sharp knife to slice it in half lengthwise. Use a spoon to scoop out the fleshy/seedy pulp.

1-inch cubes: Follow the above method, but peel the squash with a vegetable peeler before slicing it in half. Then place the squash half skin-side down against your table and make 1-inch slices across the squash. Then cube each slice.

Boiled Butternut Squash

This method yields very tender, neutral-flavored squash with no oil necessary. Though it can become watery if overcooked.

  1. Transfer the 1-inch butternut squash pieces to a large saucepan with boiling water and simmer until fork-tender (9-11 minutes usually).
  2. Then drain the water.

Steamed Butternut Squash

An oil-free method for super tender, delicately flavored squash (so more seasoning may be required in the butternut squash pasta sauce)

  1. Using either a tiered steaming pan, electric steamer, or steamer basket within a pan, spread the 1-inch cubes and steam over medium heat until tender (around 10-12 minutes).

Baked Butternut Squash

Baking butternut squash with a small amount of oil will caramelize it for extra depth of flavor and some browned crispiness. However, it won’t blend quite as smoothly, depending on how crisp it is.

  1. First, preheat the oven to 400F/205C.
  2. For the squash halves, brush a little oil over the flesh, then place the cut-side down on a parchment-lined baking tray. For the cubes, spread them across a parchment paper-lined baking tray, and toss with a bit of seasoning and oil.
  3. Then bake until tender and lightly caramelized. The halved pieces should take between 30-45 minutes (based on the size of the squash). The cubes will take 20-25 minutes.

You could also bake the butternut squash whole!

Air Fryer Butternut Squash

Air fryer butternut squash will yield similar results to baked but in less time.

Brush (or spray) the squash with a little oil/ cooking spray and seasoning:

For halved squash: Cook cut-side down at 350F/180C for 20 minutes before flipping and cook for a further 10-15 minutes, or until tender.

For cubed squash: Spread across the bottom of your air fryer basket (don’t crowd the basket, or they’ll steam, rather than caramelize), and cook for 15-20 minutes at 390F/200C, tossing every 5 minutes.

The exact size of the squash and your air fryer brand will affect the cooking time, so keep an eye on it.

completed Butternut Squash Mac n’ Cheese in a skillet with a serving separated into a small white bowl on the side against a white background

How to Make Vegan Butternut Squash Mac and Cheese?

  1. First, cook the butternut squash using one of the above methods (boil, bake, air fry).
  2. Meanwhile, prepare your pasta of choice according to the package instructions.

It’s best to do this in the last few minutes of cooking time for the squash, so the pasta is ready around the same time.

  1. Then, transfer the cooked squash to a food processor with the broth, nutritional yeast, onion, and mustard. Blend/process until smooth and creamy, then set aside.
  2. In a medium pan, melt the vegan butter over medium-low heat. Once melted, whisk in the flour, cooking for 1-2 minutes. Then gradually whisk in the non-dairy milk, butternut squash mixture, and seasonings. Continue to cook until the sauce thickens (usually 1-2 minutes). Then remove from the heat.

If it’s too thick, add in a splash of extra plant-based milk. If it’s too thin, make up a small amount of additional flour slurry to add to the sauce.

  1. Finally, fold in the pasta and enjoy warm!

For a baked butternut squash pasta bake, add a sprinkle of breadcrumbs to the top of the butternut mac and cheese along with some melty vegan cheese (optional), and broil until crisp and golden on top.

Enjoy this hearty butternut mac and cheese either alone or alongside a leafy green salad, some crusty bread, or additional roasted/broiled/grilled veggies (like broccoli, asparagus, green beans, etc.!)

How to Store?

To cut down on prep time, you can cook the butternut squash in advance and store it for 3 days in an airtight container in the refrigerator (or 3-4 months in the freezer). You could also prepare the butternut squash vegan cheese sauce in advance and store it in an airtight container for 4-5 days.

Once cooked, store the assembled vegan butternut squash mac and cheese in an airtight container, either in the fridge for several days or in the freezer for 2-3 months. Note that the sauce will thicken, and the pasta will continue to soften.

If you plan to prepare the vegan butternut squash mac and cheese specifically for meal-prep/storing, we recommend only cooking the pasta 75%, so it doesn’t become overcooked when reheated.

To reheat, you can do so in the microwave or on the stovetop, adding an extra splash of broth or plant-based milk to bring the sauce back to your desired consistency.

completed Butternut Squash Mac n’ Cheese in a skillet with a serving separated into a small white bowl on the side against a white background


  • Can I substitute the butternut squash? The most similar replacements would be other squash, pumpkin, or sweet potatoes.
  • Can I make the vegan butternut squash pasta sauce thicker/creamier? Our favorite way to do this is to add either some white beans (like cannellini, butter beans, or Great Northern) OR soaked cashews (boil them with the squash).
  • How else can I use the butternut squash cheese sauce? There are several ways to use this creamy, cheesy sauce, including over roasted veggies, adding to casseroles, using as a dip for fries, over nachos, baked potatoes, and more!
  • Is butternut squash mac and cheese healthy? Yes! Unlike regular mac and cheese, this vegan butternut squash macaroni and cheese contains no processed ingredients and high levels of dairy and fat. Instead, the squash adds tons of fiber and nutrients.
  • What does butternut squash mac and cheese taste like? Butternut squash has a slightly sweet flavor similar to pumpkin and sweet potato. When combined with the remainder of the sauce ingredients, this pasta dish is subtly sweet and savory, slightly nutty, and ever so slightly earthy, with a ‘cheesy’ finish (thanks to the nutritional yeast).

Top Recipe Tips and Notes

  • The cooking time may vary: Based on the size of the squash and your particular oven/ air fryer.
  • To cut down on prep: Feel free to use pre-chopped squash.
  • Use a high-speed blender/food processor: That way, you’ll get a super smooth and creamy butternut squash cheese sauce.
  • Cook the pasta until al dente: It will continue to soak up the sauce and soften when resting, so if you plan to leave leftovers, it can become ‘mushy.’ By cooking it al dente, it should be fine for an extra few days.
  • For a ‘goopy’ vegan cheese consistency: Use tapioca flour instead of thickening the sauce with flour. It gives the sauce an ‘elastic’ (aka melted vegan cheese) consistency.

completed Butternut Squash Mac n’ Cheese in a skillet with a serving separated into a small white bowl on the side against a white background

More Easy Vegan Pasta Recipes

Or browse through this list of 20 vegan pasta recipes you have to try! For more recipes from Margaret, check out The Plant Philosophy!

Photos by Alfonso Revilla

Butternut Squash Mac n' Cheese

5 from 33 votes
Prep: 15 minutes
Cook: 35 minutes
Total: 50 minutes
Servings: 4 servings
This vegan butternut squash mac and cheese is creamy, comforting, wholesome, and requires just 9 ingredients (plus salt & pepper)! Make this vegan mac and cheese without cashews, processed ingredients, gluten-free optional, and get ready to indulge!


  • 2 cups of butternut squash peeled & roasted or peeled, diced & boiled (about 1/2 large butternut squash)
  • 2 Tablespoons of vegetable broth
  • 1 ½ cups of nutritional yeast
  • ½ of a large white onion diced
  • 1 tablespoon of dijon mustard
  • 13.5 ounces of pasta
  • 2 Tablespoons of vegan butter
  • 1 ½ Tablespoons of all-purpose flour
  • ¾ cup of plant-based milk
  • Pinches of salt, pepper, red pepper flakes and garlic (optional)


  • Bring a large pot of water to a boil and add butternut squash. Cook for 10 -15 minutes until squash has softened and then drain out the water.
  • Place the cooked butternut squash in your food processor with broth, nutritional yeast, onion, mustard, and pulse until the mixture is smooth. Set aside.
  • Prepare pasta according to your box or bag (or however you normally do it!). Drain and set aside.
  • In a medium pan, heat vegan butter over medium-low heat until melted. Whisk in flour and let cook for 1-2 minutes. Whisk in non-dairy milk, butternut squash mixture, and any optional seasonings. Continue to whisk until the mixture begins to thicken (about 1-2 minutes). If it's too thick, add in more milk. Once thickened, remove it from the burner. Fold into pasta and serve warm, enjoy!


To roast the butternut squash instead of boiling, heat oven to 400 degrees F and place squash face down on a cooking sheet for 30-45 minutes.


Calories: 524kcalCarbohydrates: 90gProtein: 22gFat: 9gSaturated Fat: 1gPolyunsaturated Fat: 3gMonounsaturated Fat: 3gTrans Fat: 1gSodium: 188mgPotassium: 819mgFiber: 9gSugar: 5gVitamin A: 7460IUVitamin C: 16mgCalcium: 116mgIron: 3mg

Disclaimer: Although attempts to provide accurate nutritional information, kindly note that these are only estimates. Nutritional information may be affected based on the product type, the brand that was purchased, and in other unforeseeable ways. will not be held liable for any loss or damage resulting for your reliance on nutritional information. If you need to follow a specific caloric regimen, please consult your doctor first.

Additional Info

Author: Margaret Chapman
Course: Dinner
Cuisine: American
Method: Stovetop
Diet: Vegan
Tried this recipe?Please tag us at @PlantBasedOnABudget! 🙂

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. 5 stars
    I have made this sauce twice this month. The first time with an acorn squash, cuz thats what I had. Made a baked Mac n cheeze casserole with broccoli and it was great!! Went to make it again with a butternut squash last week and did the same. Had some sauce leftover and warmed on the stove tonite to dunk crispy pan fried potato wedges in. INCREDIBLY DELICIOUS!! Had to share. Thanks for this one and try it sometime!! Really good!!