Butternut Squash Mac and Cheese with Thyme Breadcrumbs (Vegan)
image of vegan butternut squash mac and cheese recipe with thyme breadcrumbs
Butternut Squash Mac and Cheese with Thyme Breadcrumbs

Cozy, delicious, and pretty simple, vegan butternut squash mac and cheese with thyme breadcrumbs. Made with roasted squash, onions & garlic.

Jump to Recipe

Cozy, delicious, and pretty simple, vegan butternut squash mac and cheese with thyme breadcrumbs. The secret to this autumnal inspired cheesy mac is the roasted butternut squash, onion, and garlic cloves. Blended with the remaining ingredients, and then tossed with the pasta. Baked together until perfection with the thyme infused breadcrumbs. Every bite is packed with cheesy, creamy pasta and a lovely crunch from the thyme breadcrumbs. This vegan cheesy mac is fancy enough for special occasions, but also easy enough to make any night of the week! Plus, it’s a great way to sneak in some vegetables.

This butternut squash Mac and cheese recipe is…

  • cozy and healthyish.
  • perfect for cold winter nights.
  • the ultimate vegan mac.

Ingredients for baked vegan butternut squash mac and cheese

  • Pasta: Use any short cut pasta of your choice! Macaroni pasta, and Spirali Pasta are my go-to’s for this recipe. If you want this recipe to be gluten-free, use your favorite gluten-free pasta!
  • Butternut squash: Peel the skin off, and cut into cubes. Once roasted, it’ll be the perfect base for our cheesy vegan sauce.
  • Onion: Just one! Chopped in quarters, and then roasted with the butternut squash.
  • Garlic: A generous amount of garlic cloves, that will be roasted and become a little caramelized will gift this vegan Mac and cheese with an incredible gourmet flavor.
  • Cashews: The raw cashews need to be soaked overnight, or for at least one hour. This will help soften up the cashews, making it easier for your food processor, high-speed blender or even immersion blender. Use boiling water to speed this process up. The cashews will help the butternut squash sauce become super thick and creamy.
  • Apple cider vinegar: A couple tablespoons for the cheesy butternut squash sauce. You could also sub for lemon juice.
  • White miso: This is optional, but it really does help build the flavor profile, and gift us with that umami flavor you traditionally taste in real cheese.
  • Tomato puree: Aka tomato puree. It’ll help give this vegan baked mac and cheese a gorgeous color, and a little of that umami tomato flavor.
  • Dijon mustard: Any brand of smooth dijon mustard!
  • Non-dairy milk: oat milk, soy milk, almond milk, or even cashew milk. Use whatever plant-based milk you have at home!
  • Nutritional yeast: It’ll gift this vegan mac and cheese with a cheesy flavor, without having to use any cheese!
  • Vegan cheese: This is optional, but I like to add in one cup of vegan grated cheese.
  • Spices: Nutmeg, smoked paprika, salt and black pepper.

Ingredients for the thyme breadcrumbs

  • Herbs: Fresh thyme leaves for the thyme breadcrumbs!
  • Breadcrumbs: Store-bought breadcrumbs. Again, if you want this recipe to be gluten-free use gluten-free breadcrumbs!
  • Oil & vegan butter: Good quality olive oil or extra virgin olive oil to roast the veggies with and a few tablespoons of vegan butter for the thyme breadcrumbs.

Roasting the veggies…

Cutting into a butternut squash or any winter squash can be a little hard. To make it a little easier, I like to pop the whole butternut squash into the microwave and cook it for only around 1-2 minutes. Cut the squash in half, peel off the skin, and then cut into medium-small chunks. Then, cut the head of a garlic bulb off, and drizzle a little olive oil over the exposed garlic cloves. Wrap it up in foil. Cut the onion into quarters and no smaller! This way, the onion will cook perfectly.

Transfer the squash chunks onto a baking sheet, along with the onions, and drizzle with olive oil. Season with salt and black pepper, and give everything a good mix. To prevent the onion from burning try and keep the quarters in tact before popping into the oven. Pop the garlic head onto the baking sheet and bake everything together for 20-30 minutes or until the butternut squash is tender.

All about the thyme breadcrumbs…

As fancy as these breadcrumbs may sound, they are super simple to make. Plus, it transforms this vegan mac into something a little more special. Melt vegan butter in a medium-large pan over medium heat. Once the butter has melted, add in the thyme leaves. Cook together for a few 1-2 minutes, then simply turn off the heat and mix in the store-bought breadcrumbs.

The butternut squash mac and cheese sauce…

Allow the veggies to cool slightly, then pop the butternut squash chunks and onions into a high-speed blender. Carefully remove the skins from the garlic and add in the caramelised garlic cloves into the blender. Add in the nutritional yeast, paprika powder, nutmeg powder, white miso paste, tomato puree, dijon mustard, apple cider vinegar, oat milk and soaked cashews. Blitz together until you are gifted with a smooth, creamy sauce. Season with a little salt and black pepper.

Final touches…

Bring a large pot of water to a boil, then add in the short cut pasta. Cook the pasta following the package directions, and cook until al dente. Drain the water, and pour in the butternut squash vegan cheese sauce over the cooked pasta. Add in the grated vegan cheese, and gently mix together until all the pasta is covered in sauce.

Transfer the butternut squash sauce covered pasta into a baking dish. Sprinkle over the thyme bread crumbs and bake for 20-30 minutes or until the bread starts to become golden. And just like that – you have a healthy, yet delicious vegan butternut squash mac and cheese recipe.

Once you try this vegan mac and cheese recipe, please leave a star rating and review below! I try my best to respond to you all. Oh, and don’t forget to tag me on Instagram – I can’t wait to see your images!!

Keep any leftovers refrigerated in an airtight container for 2-3 days.

More vegan recipes you’ll love


Butternut Squash Mac and Cheese with Thyme Breadcrumbs (Vegan)

Cozy, delicious, and pretty simple, vegan butternut squash mac and cheese with thyme breadcrumbs. Made with roasted squash, onions & garlic.

  • Prep Time: 10 minutes
  • Cook Time: 1 hour
  • Total Time: 1 hour 10 minutes
  • Yield: 8 people 1x
  • Category: Main Course
  • Cuisine: American
image of vegan butternut squash mac and cheese recipe with thyme breadcrumbs
Save Recipe
Units Scale


  • 12 tbsp olive oil
  • 4 cups cubed butternut squash
  • 1 yellow onion (cut into quarters)
  • 1 garlic bulb
  • 1/2 cup cashews (soaked in boiling water for 1 hour. )
  • 1 1/4 cup oat milk
  • 1 cup nutritional yeast
  • 1 tbsp white miso paste
  • 1 tbsp apple cider vinegar
  • 1 tbsp dijon mustard
  • 1 tbsp tomato paste/puree
  • 1 tsp paprika powder
  • 1/4 nutmeg powder
  • salt and black pepper (to taste)
  • 1 cup grated vegan cheese (optional )
  • 1 pound short cut pasta
  • 1 cup panko breadcrumbs
  • 2 1/2 tbsp vegan butter
  • 1 tbsp fresh thyme leaves


  1. Preheat the oven to 218°C/425°F.
  2. Roasting veggies: Coat the butternut squash cubes and onion with olive oil, salt and black pepper in a baking pan. Cut the head off a garlic bulb, and drizzle the exposed garlic cloves with a little olive oil. Wrap up in foil. Bake for 20-30 minutes or until butternut squash is tender.
  3. Thyme breadcrumbs: While the veggies roast, make the thyme breadcrumbs by simply heating the butter in a medium pan. Once the butter has melted add in the thyme leaves and cook for a few seconds or until fragrant. Turn off the heat and mix in the breadcrumbs.
  4. Mac and cheese sauce: Into a blender add in the apple cider vinegar, oat milk, dijon mustard, tomato puree, miso paste, nutmeg powder, paprika powder, nutritional yeast, softened cashews, the roasted butternut squash and onions. Remove the skins from the garlic and add in 7-10 cloves. Blend until smooth and then season with salt and black pepper.
  5. Final touches: Cook the short cut pasta following the package directions. Drain the water. Pour in the mac and cheese sauce over the pasta. Add in vegan cheese and mix until well combined. Transfer into a baking dish. Top with the thyme breadcrumbs and bake for 20-30 minutes or until the breadcrumbs become golden.
  6. Allow to cool slightly before serving! Enjoy!