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GF Baked Butternut Squash Mac and Cheese | Lemons and Basil
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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 9x13 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