Growing up, I would always look forward to my mom's homemade macaroni and cheese. If you're craving a healthier version of that comfort meal, you must try this Baked Vegan Butternut Squash Mac & Cheese! It's tender and gooey on the inside, golden and cheesy on the outside - and absolutely mouthwatering! Everyone will love this and no one will the cheese sauce is made from butternut squash!

Vegan Butternut Squash Cheese Sauce Ingredients
- Butternut Squash: To make the vegan butternut squash "cheese sauce" needed for this recipe, you will need one medium-sized butternut squash. this is the equivalent of about 3 heaping cups of squash.
- Onion: Use white or yellow onion to flavor the butternut squash.
- Olive Oil or Vegan Butter: Use vegan butter or extra virgin olive oil to sauté the veggies in.
- Plant-based Milk: Use plain and unsweetened almond or oat milk in this baked butternut squash macaroni and cheese recipe. If you are not vegan or dairy-free, you can use regular whole milk.
- Nutritional Yeast: Nutritional yeast gives the healthy butternut squash sauce a nice nutty and cheesy flavor without the need to use actual cheese.
- Salt and Pepper: Used to flavor the healthy vegan butternut squash mac and cheese.
- Water: Used to boil the squash to create the cheese sauce before baking.
Macaroni Ingredients
- Elbow Pasta: You may use vegan, regular, or gluten free pasta in this baked butternut squash mac and cheese. For gluten-free elbow pasta, I used the brand Jovial.
- Water: Used for boiling the elbow pasta.
- Olive Oil: Extra virgin olive oil is used in the pasta water to keep the noodles from sticking. Avocado oil will work too.
- Salt: To season the pasta water and give it flavor.
Baked Butternut Squash Mac & Cheese Toppings
- Vegan Shredded Cheese: I prefer shredded vegan cheddar cheese or Colby cheese in this butternut squash mac and cheese. The brand I used was VioLife and the cheese got very melty in the oven. If you are not vegan or dairy free, you can use regular shredded cheese.
- Olive Oil Spray: Helps the vegan cheese melt in the oven - a little trick I learned when I first cut out dairy!
How To Make Vegan Butternut Squash Mac & Cheese
Step 1: Carefully slice your butternut squash in half, lengthwise. Peel the skin off the outside. Use a spoon to remove the guts and seeds from the center and then slice the squash into one inch slices.
Step 2: Bring a medium saucepan with olive oil to medium heat. Add the onions and cook until lightly golden. Then, add the squash and cook for about 5 minutes.
Step 3: Add water to the pot, bring to a low simmer, cover, and cook the squash for 20 minutes or until tender. While the squash cooks, boil your elbow pasta in a large saucepan. Once tender, drain it from the pasta water, leaving about 2-4 tablespoons of pasta water in the pot with the noodles. Set aside.
Step 4: Drain the squash and add it back into the saucepan to be blended with your handheld immersion blender. If you do not have an immersion blender, add the squash directly into your blender.
Step 5: Add the nutritional yeast, non dairy milk, salt and pepper and then use a blender to blend the squash until creamy. This is used as our cheese sauce. Pour the creamy butternut squash cheese sauce over the cooked noodles.
Step 6: Mix the sauce with the noodles and then transfer them all into a greased baking dish. Top with shredded vegan cheese and spray with olive oil.
Step 7: Bake in the oven until golden - about 30 minutes. Broil for 2 minutes at the end to brown the cheese. Enjoy warm.
Frequently Asked Questions
Delicious! Thanks to the nutritional yeast, it has a nutty cheesy taste. The butternut squash cheese sauce is creamy and lightly sweet.
Absolutely! Sprinkle vegan or gluten-free breadcrumbs on top of the dish before baking in the oven to give it that classic bread crumb mac and cheese texture.
This vegan butternut squash mac and cheese recipe is plant-based, includes hidden healthy ingredients like squash and nutritional yeast, and contains little to no saturated fat! This is a healthier alternative to that classic comfort dish that everyone loves.
Vegan Butternut Squash Mac & Cheese
Equipment
- 1 large saucepan
- 1 Medium Saucepan
- 1 10-12 inch casserole dish
- 1 handheld immersion blender or standing blender
- 1 Strainer
Ingredients
Macaroni Ingredients
- 1 tablespoon extra virgin olive oil
- a pinch of salt
- 12 oz box of elbow pasta gluten-free if needed
Butternut Squash Sauce
- 1 tablespoon extra virgin olive oil or vegan butter
- ¼ cup diced yellow or white onion
- 1 medium butternut squash
- 3 cups water
- 1 cup plain and unsweetened almond or oat milk
- ¼ cup nutritional yeast
- 1 teaspoon salt
- ¼ teaspoon black pepper
Butternut Squash Mac & Cheese Toppings
- 1 cup vegan shredded cheddar cheese or shredded colby cheese
- olive oil or avocado oil spray
- salt and pepper
Instructions
Vegan Butternut Squash Mac & Cheese Instructions
- Begin by slicing your butternut squash in half, carefully. Use a vegetable peeler to peel the skin off. Use a spoon to scoop out the seeds and guts of the squash. Slice the squash into 1 inch cubes. Set aside.
- To make the butternut squash sauce, bring a large saucepan with olive oil or vegan butter to medium heat. Once warm, add the onions and cook, stirring, until tender (about 2-3 minutes).
- Add the butternut squash and cook for about 5 minutes or until it begins to lightly brown. Add water until the squash is completely covered. Bring the pot to a low simmer, cover, and cook for 20 minutes.
- While the butternut squash cooks, prepare the pasta. Bring a medium saucepan with olive oil and water to a boil. Add the pasta and cook, as instructed on the packaging, until tender. Strain, reserving 2-4 tablespoon of the pasta water. Set aside.
- Once the butternut squash has simmered for 20 minutes, uncover and strain. Transfer the squash back into the pot so that you can use a handheld immersion blender to blend the cheese sauce. If you don't have an immersion blender, you can add the squash into a regular blender along with the following ingredients. Add the almond milk or oat milk, nutritional yeast, salt, and pepper. Use a handheld immersion blender to blend until creamy and silky smooth. Pour the sauce over the cooked pasta and stir.
- You can enjoy the butternut squash macaroni just like this or you can continue to the next step for baking.
Baking the Butternut Squash Mac & Cheese
- Preheat the oven to 375. Grease a casserole dish with vegan butter or olive oil spray.
- Pour all of the butternut squash macaroni noodles into the dish. Top with shredded vegan cheese. Spray the top with olive oil spray to help the vegan cheese melt. Bake in the oven for 20 minutes. Option to broil for 2 minutes at the end.
Mireille says
Super yummy! Reminded me of an old fashioned decadent mac and cheese. My family loved it and requested I make it again. At first I thought there was too much sauce, but during the baking the sauce gets sucked up and it’s perfect. Also the baking and broiling really adds a ton to it, so don’t skip it.