GF Baked Butternut Squash Mac and Cheese

GF Baked Butternut Squash Mac and Cheese | Lemons and Basil

This GF Baked Butternut Squash Mac and Cheese is a healthier spin on the more traditional dish. It’s rich and cheesy and full of so much savory goodness – perfect for Thanksgiving!

I love the traditions that come with the holidays. The special gatherings with family and friends year after year. The chance to annually do the same customs, reflecting on the past while embracing the present. These moments aren’t always perfect, nor Instagram worthy, but there’s something comforting about familiarity. Something sweet about creating these same memories year after year with our kiddos.

Many of the family traditions on my side of the family have altered over the last five years. Between the loss of my mom in 2016 and the birth of our two little ones, life has changed in many ways.  Many of those traditions are centered around gathering and eating together. My dad has actually become quite skilled in the kitchen. My mom always enjoyed cooking and so throughout their marriage, there was no need for him to do much in the way of preparing food.

GF Baked Butternut Squash Mac and Cheese | Lemons and BasilGF Baked Butternut Squash Mac and Cheese

But when she got sick in 2013, he didn’t have much choice. It was learn to cook, or spend way too much on takeout. Since then, he’s learned to fend for himself quite nicely on a daily basis. And has pretty much mastered my grandmother’s homemade butterhorn rolls! He also typically handles the meat and potatoes at our family gatherings, which always turn out wonderful. Occasionally my sister or I make the the potatoes, but more often than not he seems to enjoy providing these things for the family. My sister and I fill in with an array of sides, veggies, and desserts.

Life is so different with mom. Not a birthday, holiday or other family gathering passes where we don’t grieve her absence. Each one thinking how different life would be if she were still here. And yet, God is so gracious. We’ve each found our new role. We have little ones and teenagers that bring us joy and laughter. We find ways to remember and honor her at each of these gatherings.

In a year where there have been SO many HARD things, it takes such intention to step back and see the good. To see and acknowledge His goodness. And I think this Thanksgiving, perhaps more than most, I find myself sitting in that truth. He is good.

GF Baked Butternut Squash Mac and Cheese | Lemons and Basil

Mac and cheese is one of my niece’s favorites and a dish that often graces our Thanksgiving spread. Thankfully, no one in my family has a gluten intolerance. But when it comes to our Friendsgiving gathering, there are more than a few who aren’t able to eat gluten. And honestly, I personally prefer the chickpea pasta to traditional wheat based pasta. It’s higher in fiber and protein and the taste and texture is so similar that I’ve found I can pretty easily satisfy even the pickiest of eaters with it. I also just love knowing I have a great allergy-friendly option. So it was the natural choice for this GF Baked Butternut Squash Mac and Cheese.

Reasons to Love this GF Baked Butternut Squash Mac and Cheese:

  • Loaded with cheese, a necessity for Mac and CHEESE
  • Hidden veggies
  • Gluten-free, made with chickpea pasta that offers a great source of protein and fiber!
  • Sage, thyme and garlic bring such a lovely dose of savory goodness
  • Healthy enough (hello chickpea pasta + butternut squash) to not feel bad about, yet rich, delicious and Thanksgiving dinner worthy!

As with nearly every recipe I share here, I gathered my ingredients at Sprouts. I love Sprouts year round, but especially during the holidays. They have so many fun specialty finds like Pumpkin Snaps, Pumpkin Seed Tortilla Chips, and Sweet Harvest Pumpkin Holiday Tea to name a few. But even more important than the fun packaged things, they have the best array of fresh produce, and a large assortment of healthy staples with many allergy-friendly options. From the chickpea pasta, to the fresh herbs and blend of three different cheeses, I can always what I need!

GF Baked Butternut Squash Mac and Cheese | Lemons and BasilGF Baked Butternut Squash Mac and Cheese | Lemons and Basil

With Thanksgiving just around the corner, it’s likely to be a day of mixed emotions for many. For some, like myself, it’s a day of reflection on the hard and challenging things of our current situation, while acknowledging His goodness, and just how fortunate and blessed our family has been in this season.

And for others, it may be a day that highlights all the more the pain they’re experiencing from the loss of a loved one, or the loss of jobs. With the Covid pandemic, traveling and gathering with family and friends is so much trickier than it’s been in the past. But I pray each and every one of you are with loved ones. And that you find reasons to smile and have joy. I’m thankful for my little space here, and so grateful for those who have followed along these last 7 years. 💛

GF Baked Butternut Squash Mac and Cheese | Lemons and BasilGF Baked Butternut Squash Mac and Cheese | Lemons and Basil

GF Baked Butternut Squash Mac and Cheese | Lemons and Basil

Print Recipe

5 from 1 vote

GF Baked Butternut Squash Mac and Cheese

This GF Baked Butternut Squash Mac and Cheese is a healthier spin on the more traditional dish. It’s rich and cheesy and full of so much savory goodness – perfect for Thanksgiving!

Prep Time15 mins

Cook Time40 mins

Course: Dinner, Lunch, Side

Cuisine: American

Keyword: Butternut Squash, Chickpea Pasta, gluten-free, Thanksgiving

Servings: 12 people

Calories: 407kcal

Author: Kaylee Pauley


  • High speed blender


Cheesy Butternut Squash Sauce:

  • 4 tbsp unsalted butter
  • 5-6 fresh sage leaves
  • 3-4 fresh thyme sprigs
  • 3/4 cup yellow onion diced
  • 4 large cloves garlic minced
  • 4 cups butternut squash peeled and cubed
  • 2 tsp dried sage
  • 1 tsp dried thyme
  • 1 tsp sea salt
  • 1/4 tsp black pepper
  • 1 1/2 cups vegetable broth
  • 2 cups milk
  • 8 oz sharp white cheddar cheese shredded
  • 4 oz Smoked Gouda shredded
  • 4 oz Parmigiano Reggiano shredded, reserving 1/2 cup

Chickpea Pasta:

  • 16 oz 2 boxes Sprouts Brand Organic Chickpea Fusili

Crumb Topping:

  • 1/2 cup almond flour
  • 1 tbsp unsalted butter melted
  • 1/4 cup chopped fresh sage
  • pinch sea salt + black pepper


  • Preheat oven to 350 degrees.

  • Add 4 tbsp butter to a large dutch oven over medium heat. Gently stir as it begins to melt and toss in 5-6 fresh sage leaves and 2-3 fresh thyme sprigs. Stir and saute herbs for 1-2 minutes. Remove herbs, set on paper towel and reserve until later. Add the 3/4 cup diced onions and 4 minced garlic cloves to melted butter and cook 3-4 minutes or until softened.

  • Once onions are translucent, add 4 cups butternut squash, 2 tsp dried sage, 1 tsp dried thyme, 1 tsp sea salt and 1/4 tsp black pepper, stir to combine. Add 1 1/2 cups vegetable broth and the reserved herbs (previously cooked in butter), and bring to a boil. Reduce heat to low and simmer 9-10 minutes, stirring occasionally, until the squash is tender.

  • Remove the herbs and discard. Stir in the milk, then transfer mixture to a high-speed blender and puree until smooth.

  • Meanwhile, cook pasta according to package direction – bringing water to a boil in a large pot, then adding pasta and cooking 6-7 minutes, leaving them just slightly undercooked, as they’ll continue to cook in the oven. Once pasta is cooked, drain and set aside.

  • Add the pureed sauce back to the dutch oven on medium heat. Grate 8 oz white cheddar cheese, 4 oz smoked gouda and 4 oz Parmigiano Reggiano, reserving 1/2 cup of the Reggiano. Add shredded cheese a handful at a time, stirring well between each addition to ensure it melts smoothly. Stir in the pasta. Taste and add additional seasoning if desired.

  • Spray 9×13 glass or ceramic dish with nonstick spray. Add the cheesy butternut squash pasta mixture to the dish, then top with the remaining 1/2 cup Reggiano and lightly stir.

  • In a small bowl, stir together 1 tbsp melted butter, 1/2 cup almond flour, 1/4 cup chopped sage, 1 tsp fresh thyme, pinch sea salt and pepper, and sprinkle over the top.

  • Bake for 15 minutes, then broil another 1-2 minutes until the crumb topping is golden brown. Watch closely to make sure it doesn’t burn.

  • Serve immediately and enjoy!


Serving: 1g | Calories: 407kcal | Carbohydrates: 35g | Protein: 20g | Fat: 20g | Saturated Fat: 12g | Polyunsaturated Fat: 0.2g | Monounsaturated Fat: 1.2g | Cholesterol: 53mg | Sodium: 546mg | Potassium: 693mg | Fiber: 7.5g | Sugar: 5g | Vitamin A: 107IU | Vitamin C: 18mg | Calcium: 164mg | Iron: 4mg

Inspired by Blue Bowl’s Baked Butternut Squash Mac and Cheese.

This post is sponsored by Sprouts Farmers Market, but all opinions are my own. Thanks for supporting the brands that keep Lemons and Basil in action!

We will be happy to hear your thoughts

Leave a reply

Grocery Demo
Compare items
  • Total (0)
Shopping cart