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This Butternut Squash Mac and Cheese is rich, creamy, and 100% vegan. It uses roasted vegetables and plant-based cheese to create a comforting, dairy-free meal that everyone will love. It’s topped with a garlicky everything bagel seasoning bread crumb topping to take it to the next level. The roasted squash gives natural sweetness and depth, while the vegan cheddar adds a bold, cheesy flavor. This is the perfect autumn comfort meal the whole family will love!

bowl of creamy vegan butternut squash mac and cheese topped with everything bagel panko bread crumbs and parsley

Table of Contents

butternut squash, non-dairy milk, salt, pasta, everything bagel seasoning, nutritional yeast, olive oil, onion powder, black pepper, vegan butter, nutmeg, garlic powder, breadcrumbs, parsley, vegan cheese, lemon, garlic, shallot

Ingredients to Make Butternut Squash Mac and Cheese

  • Pasta – Choose any pasta you like, but rigatoni, elbows, shells, or cavatappi hold the sauce best.
  • Olive Oil – Adds richness and helps roast the vegetables evenly.
  • Butternut Squash – The heart of the sauce. When roasted, it becomes creamy, slightly sweet, and full of flavor.
  • Shallots – Brings a mild onion flavor that deepens when roasted.
  • Garlic – Adds a roasted, nutty base flavor to the sauce.
  • Nutritional Yeast – Provides a cheesy, umami taste without dairy.
  • Lemon Juice – Balances the flavors and brightens the sauce.
  • Garlic and Onion Powder – Add savory depth to enhance the flavor of the roasted vegetables.
  • Nutmeg – A small amount boosts warmth and complements the squash.
  • Salt + Black Pepper – Essential for seasoning and balance.
  • Non-Dairy Milk – Creates a silky sauce. Use unsweetened almond, oat, or soy milk.
  • Vegan Cheddar Cheese – Adds creamy texture and a sharp, cheesy taste.
  • Vegan Butter – Used for the breadcrumb topping. Adds flavor and helps achieve crispness.
  • Panko Breadcrumbs – Create a crunchy layer on top.
  • Everything Bagel Seasoning – Adds texture and flavor from sesame, poppy seeds, garlic, and onion.
  • Parsley – Freshens up the dish with color and light flavor.

How to Make Butternut Squash Mac & Cheese

slicing butternut squash
butternut squash seasoned with salt and pepper on a baking sheet
garlic seasoned with oil and salt in foil
shallots seasoned with oil and salt in foil
butternut squash, garlic, and shallots on a baking sheet
  • Roast the Vegetables
    • Preheat oven to 400°F.
    • Halve the squash, drizzle with oil, and season with salt.
    • Wrap shallots and garlic in foil with oil and salt.
      Roast altogether for about 40 minutes, until tender.
adding garlic to melted butter
adding panko bread crumbs to melted butter
toasting bread crumbs in pan
browning panko breadcrumbs in skillet
  • Make the Everything Bagel Breadcrumb Topping
    • Melt vegan butter in a pan.
    • Add minced garlic, cook for 1 minute.
    • Stir in breadcrumbs until golden.
    • Mix in everything bagel seasoning and parsley.
  • Cook the Pasta
    • Boil salted water and cook pasta until al dente.
    • Reserve one cup of pasta water. Drain and set aside.
adding nutritional yeast to the blender
adding ingredients to a blender and starting to blend
blending sauce
  • Make the Sauce
    • Blend roasted squash, shallots, garlic, nutritional yeast, lemon juice, seasonings, and non-dairy milk until smooth and creamy.
pouring sauce into a large skillet
adding cheese to skillet
creamy pasta in large skillet
  • Combine
    • Pour sauce into a large pot over medium heat.
    • Add pasta and vegan cheddar. Stir until melted and creamy.
    • Adjust the thickness with pasta water.
creamy mac and cheese in bowl
adding everything bagel bread crumb topping
finished bowl of butternut squash mac and cheese
  • Serve
    • Spoon into bowls.
      Top with the breadcrumb mixture and enjoy warm.

*Find the measurements and step-by-step instructions in the recipe card down below

Equipment Needed

  • Chef’s knife – for cutting the squash, shallots, and garlic.
  • Cutting board – for safe and clean chopping.
  • Baking sheet – to roast the squash, shallots, and garlic.
  • Aluminum foil – to wrap the shallots and garlic for roasting.
  • Blender or food processor – to create a smooth, creamy sauce.
  • Large pot – for boiling pasta.
  • Strainer – to drain the cooked pasta.
  • Medium pan – to prepare the breadcrumb topping.
  • Wooden spoon or spatula – for stirring sauce and pasta.
  • Mixing bowls – for combining breadcrumbs and seasoning.
bowl of creamy vegan butternut squash mac and cheese topped with everything bagel panko bread crumbs and parsley

Tips and Tricks

  • Use pre-cut squash to save time on preparation. Adjust the cooking time as needed.
  • Roast extra garlic for future recipes or use it in spreads.
  • For a gluten-free version, use gluten-free pasta and breadcrumbs.
  • If the sauce thickens too much, thin it with more non-dairy milk or pasta water.
  • Add spinach or kale for an extra boost of greens.
bowl of creamy vegan butternut squash mac and cheese topped with everything bagel panko bread crumbs and parsley

Storage and Reheating

  • Store leftovers in an airtight container in the refrigerator for up to 4 days.
  • Reheat on the stove with a splash of non-dairy milk to restore creaminess.
  • Store the sauce separately in the freezer for up to 2 months. Thaw overnight and reheat before mixing with pasta.
bowl of creamy vegan butternut squash mac and cheese topped with everything bagel panko bread crumbs and parsley

Frequently Asked Questions

Can I make this nut-free?

Yes. Use oat or soy milk and ensure your vegan cheese is nut-free.

Can I use canned squash or pumpkin?

Yes, but roasted fresh squash gives the best flavor and texture.

Do I need the breadcrumb topping?

It’s optional, but it adds crunch and flavor contrast to the creamy sauce.

What if I don’t have everything bagel seasoning?

Use plain panko with garlic powder, sesame seeds, and a pinch of salt.

This Butternut Squash Mac and Cheese is simple, nourishing, and perfect for cozy nights. It tastes rich and cheesy, yet uses only plant-based ingredients. Make it for dinner, meal prep, or a family favorite that everyone will ask for again.

Craving More Pasta?

Make sure you tag us on Instagram @sweetsimplevegan and @consciouschris and hashtag #sweetsimplevegan if you recreate any of our recipes, we love to see your photos!

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bowl of creamy vegan butternut squash mac and cheese topped with everything bagel panko bread crumbs and parsley

Creamy Vegan Butternut Squash Mac and Cheese

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5 from 1 review

  • Author: Sweet Simple Vegan
  • Total Time: 1 hour 10 minutes
  • Yield: 4–6 servings 1x
  • Diet: Vegan
Print Recipe

Description

This Butternut Squash Mac and Cheese is rich, creamy, and 100% vegan. It uses roasted vegetables and plant-based cheese to create a comforting, dairy-free meal that everyone will love. It’s topped with a garlicky everything bagel seasoning bread crumb topping to take it to the next level. The roasted squash gives natural sweetness and depth, while the vegan cheddar adds a bold, cheesy flavor. This is the perfect autumn comfort meal the whole family will love!

Ingredients

  • 1 lb pasta of choice

Sauce:

  • Olive oil
  • 1 medium butternut squash (2 cups mashed)
  • 2 medium shallots
  • 1 bulb of garlic
  • ¼ cup nutritional yeast
  • 1 tablespoon lemon juice
  • ½ teaspoon garlic powder
  • ½ teaspoon onion powder
  • ¼ teaspoon nutmeg
  • 1 teaspoon salt
  • ½ teaspoon black pepper
  • 1 cup non-dairy milk
  • 8 ounces vegan cheddar cheese

Breadcrumb topping:

  • 1 tablespoon vegan butter
  • 2 cloves garlic, minced
  • 1 cup (80g) panko breadcrumbs
  • 2 tablespoons everything bagel seasoning
  • 1 tablespoon parsley, chopped

Instructions

Roast Vegetables

  1. Preheat the oven to 400˚F.
  2. Cut the butternut squash in half lengthwise and scoop out the seeds. Drizzle with oil, sprinkle with salt, and lay both halves on a baking sheet, flat side down. 
  3. Trim the ends of the shallots, peel, then place on a sheet of aluminum foil. Drizzle with olive oil, sprinkle with salt, and wrap tightly. Lastly, remove the flaky outer layers of the garlic, then cut the top off the head of garlic, revealing the cloves. Place on a sheet of foil, drizzle the exposed cloves with oil, and wrap in foil.
  4. Place the shallots and garlic on the baking sheet with the squash and put them in the oven. After 40 minutes, remove the garlic and shallots from the oven and check if the squash is fork-tender. If not, bake for another 10 minutes, or as needed.

Prepare Breadcrumb Topping

  1. In a medium pan over medium heat, melt the vegan butter. Once melted, add the garlic and sauté for 1-2 minutes, stirring frequently to prevent burning. 
  2. Add the breadcrumbs and sauté for another 4-5 minutes, until golden brown. 
  3. Remove from heat and add the everything bagel seasoning and parsley. Stir together and set aside.

Assemble

  1. Bring a large pot of water to a boil and salt generously. Add the pasta and cook until al dente, stirring occasionally.
  2. Before draining the pasta, reserve 1 cup of pasta water and set aside.
  3. Meanwhile, add 2 cups of butternut squash, the roasted shallots, roasted garlic, nutritional yeast, lemon juice, garlic powder, onion powder, nutmeg, salt, black pepper, and non-dairy milk to a blender. Blend until smooth.
  4. Add the blended mixture to a large pot over medium heat and bring to a simmer. 
  5. Add the cooked pasta and vegan cheese and mix together. Continue cooking, stirring frequently, until all the cheese is melted and the pasta is coated. If the sauce is too thick, add some pasta water as needed. Add salt and black pepper to taste.
  6. Serve and top with the breadcrumb topping.

Notes

  • Storage: Keep leftovers in an airtight container in the fridge for up to 4 days.
  • Reheating: Heat on the stove with a splash of non-dairy milk to restore creaminess.
  • Freezing: Store the sauce separately in the freezer for up to 2 months. Thaw overnight and reheat before mixing with pasta.
  • Prep Time: 10 minutes
  • Cook Time: 60 minutes
  • Category: Dinner
  • Method: Stove Top and Oven

Meet The Bloggers

hey there! we’re jasmine & chris.

Hi, we’re Jasmine and Chris! We share fresh and fun recipes to show you that vegan cooking is easy, approachable and delicious. When we’re not blogging, you will probably find us enjoying live music, tending to our backyard garden or playing with our dogs Berry and Louie

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1 Comment

  1. Made this for dinner and it was awesome! I did replace the toasted breadcrumbs with some crispy, shredded tofu. I will totally make this again!

    Reply