Butternut Squash Baked Mac and Cheese

This gluten-free butternut squash baked mac and cheese is a great way to add more vegetables into a classic comfort dish! Plus, the butternut squash gives the entire dish a beautiful, natural golden orange color. The mac and cheese is always a favorite at home and at my cooking classes!

Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs

Note: This is an updated version of the butternut squash baked mac and cheese that I published in March 2016. I simplified the cooking method and added a video tutorial on how to make the dish. 

My body’s in a bit of a funk. Nothing serious. I’m just having one of those “why am I waking up before sunrise?” kind of moments. This probably tells you two things about me: (1) I’m not a morning person; and (2) I’ll never get used to this whole Spring Forward thing.

It’s these moments when I need something to ground me, to make me feel like everything is okay. These are the times that call for a good ‘ol mac and cheese.

Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs

When I started transitioning over to a gluten-free diet last summer, I thought that I would miss pasta very much. I had heard about how bad gluten-free pastas could be—how they turn gummy and mushy when you try to cook them. My first ever gluten-free pasta was from Trader Joe’s, and the results were less than stellar. (Sorry, TJ! I love you for many other things, like your dried mangos and coconut oil, but I’ll give the gluten-free pasta a pass.)

After trying out quite a number of brands, I’ve found that Ancient Harvest, Tru Roots, Bionaturae and Jovial to be quite good for this baked mac and cheese.Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs

Why all this talk about gluten-free pasta brands? Well, I’m sharing this butternut squash baked mac and cheese creation over at Better Homes and Gardens’s Delish Dish blog today! I’ve been a huge fan of BHG for a long time, and I was incredibly honored when they asked me to guest post on Delish Dish.

For my post, I was asked to select a recipe from their immense recipe library and add my own spin to it. This Three-Cheese Baked Mac was just begging to be cooked. You can never say “no” to a good mac and cheese, right?

I made a number of changes to the original recipe, including cutting the amount of cheese in half, using gluten-free pasta, and adding a butternut squash puree to the dish. The butternut squash puree move was inspired by my friend Sabrina and her baked mac with carrot. The idea of adding a bit of sweetness to a mac and cheese dish sounded so intriguing, I had to try it for myself. Friends, butternut squash in mac and cheese tastes PHENOMENAL.


  • Substitutions: This recipe works well with pumpkin puree!
  • Adding Broccoli: I made a version of this with chopped up broccoli florets, and it tasted great. I mixed some of the florets into the mac and cheese and spread some on the top. The florets at the top get nice and crunchy!



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Butternut Squash Baked Mac and Cheese

Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs

This butternut squash baked mac and cheese is great with about 1/2 to 3/4 cup of chopped broccoli florets on the top, too. Adapted from Better Homes and Gardens.

  • Author: Lisa Lin
  • Prep Time: 10 minutes
  • Cook Time: 33 minutes
  • Total Time: 43 minutes
  • Yield: 6 Servings


  • 1 pound (450g) gluten-free penne pasta (use regular penne if not gluten free)

Cheese Sauce

  • 2 tablespoons unsalted butter
  • 2 tablespoons gluten-free all-purpose flour
  • 2 cups (475ml) low-fat milk (I used 2% milk)
  • 1 teaspoon dried oregano
  • 1 teaspoon dried thyme
  • 1/2 teaspoon black pepper
  • 1 teaspoon salt
  • 1 1/4 cups butternut squash puree (pumpkin puree also works)
  • 1 cup shredded part-skim mozzarella cheese (about 3.8 ounces/110g)
  • 1 cup shredded white cheddar cheese (about 3.8 ounces/110g)
  • 1/3 cup shredded parmesan cheese (about 2.3 ounces/65g)
  • olive oil for greasing baking dish
  • finely chopped parsley for topping (optional)


  1. Cook pasta according to package instructions. Drain pasta and rinse under cold water.
  2. Position an oven rack to the center. Preheat oven to 350ºF (175ºC). Grease a baking dish with olive oil. Set aside.
  3. Melt 2 tablespoons of butter in sauté pan over medium-high heat. Add flour and stir immediately until a soft paste, or roux, forms. Add milk and begin to stir everything immediately to prevent the roux from clumping up too much.
  4. Once the milk boils, reduce heat to medium-low and let the sauce simmer for about 3 to 4 more minutes, until the sauce thickens. Reduce the heat to low.
  5. Add the oregano, thyme, black pepper and salt and stir. Add the butternut squash puree and mix until everything is incorporated. Mix in 3/4 cup of mozzarella, 3/4 cup of white cheddar. Save the rest of the cheese for topping later. Turn off heat. Stir in the cooked pasta, until it’s well coated with the butternut squash cheese sauce.
  6. Pour mac and cheese into the prepared baking dish. Top with remaining mozzarella, white cheddar and parmesan. Bake for 15 minutes, then broil for 4 minutes to brown the cheese on top.
  7. Top finished mac and cheese with chopped parsley. Serve immediately.


NUTRITION INFORMATION: Makes 6 Servings. Amount per serving: Calories: 495, Total Fat 18g, Saturated Fat: 10g, Sodium: 764mg, Cholesterol: 52mg, Total Carbohydrate: 59g, Dietary Fiber: 10g, Sugar: 9g, Protein 24g

*In the original method, I made a butternut squash puree by sauteing 2 cups of cubed butternut squash (11 ounces) in a pan with a tablespoon of olive oil, a few cloves of crushed garlic, a splash of water and salt. The squash will need 10 minutes to cook, covered. If the water evaporates before the squash is ready, add another splash of water. Then, I blended everything in a food processor until smooth. I thought that this method was more time consuming than adding pre-made butternut squash puree into the cheese base, so I rewrote the recipe.


  • Serving Size: 6

Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs


Butternut Squash Baked Mac and Cheese - gluten free and healthier version! by @healthynibs

36 thoughts on “Butternut Squash Baked Mac and Cheese

  1. GiGi Eats

    Oh butternut squash – how I love thee more than words can describe. And in this dish I bet you give the mac and cheese a magical hint of sweetness!

  2. Traci | Vanilla And Bean

    Augh, that daylight savings is tough. I’m still feeling it Lisa! I love this transition to Spring recipe. There’s still so much winter squash around here and in my fridge! So this is perfect. I’ve not tried hardly any GF brands because I’m not GF, but if ever that has to change, I’ll be on the lookout for Jovial and Tru Roots. Congratulations on your guest post! A lightened up favorite is always handy. Heading over there now. Thank you for this my dear!

  3. Michelle @ Vitamin-Sunshine

    I actually really like Trader Joe’s brown rice pastas! I think they are nice and chewy. I also love Ancient Harvest Quinoa pasta– but I’ve never tried Tru Roots. WIll give it a shot.

    I actually really missed pasta when I first went gluten-free– but after 4 years, I almost never think of pasta. When I make it my husband is so excited because it’s like a twice a year thing! But Mac ‘n Cheese… oooh.

  4. Jan

    I have to tell you that this is probably the 12th Mac and Cheese recipe that I have tried, in order to find the perfect one. This is it! Not only is it great tasting, I got it by my 2 grandchildren who are connoisseurs of the mac and cheese.
    The addition of the butternut squash puree is brilliant and lends a sweetness to the dish, that no one could detect. Especially for children, its a great way to add extra veggies to a meal. I did not have mozzarella on hand so I used a creamy Havarti along with the cheddar cheese. I also omitted the oregano, worried that it might be over powering for the kids. I did keep the thyme, but reduced it by half. Added a couple more cloves of garlic…yum.
    Thank you for such a fabulous rendition of a classic. We all loved it…bring on more!

    1. Lisa Lin Post author

      Jan, thank you very much for trying my recipe and for your sweet comment! I’m so pleased that you and your grandchildren enjoyed the mac and cheese. I haven’t tried it with harvarti yet, but it’s definitely on the list. Honestly, reading your comment made my day! Thank you!

  5. Kortnie

    I absolutely love this recipe and my family enjoys it as well. Only thing I did different was add Gouda cheese instead of the white cheddar(I couldn’t find it shredded) and pure request of the man in the house who needs meat, I added crab meat into the mixture and topped with bacon crumbles on top. It’s a favorite in our house now!

    1. Lisa Lin Post author

      Kortnie, thank you so much for trying it!! Oh my goodness, crab meat sounds wonderful in this casserole! I’m so glad that you and your family are enjoying this!

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    1. Lisa Lin Post author

      Hi Amy, I think it should work with soy milk instead of regular milk. Are you dairy free? If you’re also substituting the cheese for dairy-free cheese and using soy milk, I’m not sure how everything will turn out.

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  8. Amanda

    Hi Lisa, I’m making this for thanksgiving tomorrow and I just realized it says to serve immediately. Will it still be ok if I reheat it tomorrow?

    1. Lisa Lin Post author

      Hi, Amanda! Yes, it will. Just reheat it at 350 degrees F for about 10 to 15 minutes, until everything is heated through. Let me know how it turns out!

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  12. Dana

    I LOVE this recipe! Made it before as written and 6 adults and 1 child finished off the entire dish in one night! I’m going to do some experimenting and see about making this recipe into the newly infamous mac and cheese hamburger buns! Fingers crossed it works!! If not I at least know the recipe is to die for!!

  13. Katie

    Hi Lisa!
    I used almond milk instead of regular milk (because it’s what I had on hand) – I also added about a tablespoon of corn starch to make sure the mixture would thicken enough. I used pumpkin (again, what I had on hand) but next time will use butternut purée and a sharper cheddar for more flavor but overall loved the recipe!

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  16. Donna

    This recipe is really looks awesome. The videos are really very helpful. I’m going to try it soon. Thanks for putting it together.


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