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a close up of bowl of gluten free butternut squash mac and cheese
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4.67 from 3 votes

Creamy Butternut Squash Macaroni & Cheese (Gluten Free)

Super creamy, cheesy and delicious Gluten-Free Butternut Squash Macaroni and Cheese with a flavorful breadcrumb topping!
Prep Time25 mins
Cook Time30 mins
Total Time55 mins
Course: Entrées
Cuisine: American
Diet: Gluten Free
Servings: 4
Calories: 638kcal
Author: Kristen Wood


  • 8 oz gluten free elbow macaroni
  • 10 oz bag frozen butternut squash
  • 1/2 cup water
  • 2 tbs butter
  • 3 tbs gluten free flour
  • 1/8 tsp ground nutmeg
  • 1/2 cup sour cream + 1 1/2 cups water blended
  • 1 tbs fresh chopped rosemary
  • Salt & cayenne
  • Olive oil for greasing casserole dish
  • 1 1/2 cups shredded sharp cheddar cheese
  • 1/2 cup shredded parmesan cheese
  • Breadcrumb Topping:
  • 3/4 cup gluten free breadcrumbs* I made mine using my magic tahini seed bread, link below
  • pinch of salt
  • pinch of freshly chopped rosemary
  • dab of melted butter


  • Cook elbow macaroni according to package directions, drain well. Set aside.
  • Add butternut squash to a food processor or blender & puree until smooth. Add 1/2 cup of water & blend again. Set aside.
  • In a large skillet or saucepan over medium heat, add the butter.
  • When butter is melted, add your gluten free flour & whisk. Add nutmeg.
  • Cook for 3-5 minutes, whisking constantly.
  • Add your water/sour cream mixture, and whisk until smooth. T
  • urn heat to high & bring to a boil while continuing to whisk. After your sauce has thickened, turn heat to low & then whisk in your butternut squash mixture.
  • Stir in fresh rosemary.
  • Add cooked elbow macaroni to the pan & then stir until noodles are well coated. Turn off heat.
  • Season with salt & cayenne (to taste).
  • Prepare your gluten free breadcrumb* topping by stirring in a pinch of rosemary, a pinch of salt & a dab of melted butter into your breadcrumbs & then tossing to coat. Set aside.
  • Preheat oven to 400° F.
  • Grease a casserole dish (I used a round 8").
  • Pour half of the macaroni noodles mix into the pan.
  • Sprinkle half of the sharp cheddar/parmesan mix over the noodles.
  • Add the remaining noodles & then top with the rest of the cheese mix.
  • Sprinkle your prepped breadcrumbs on top.
  • Place your pan in a 400° F oven & bake for 30 minutes, or until bubbling & beginning to brown.
  • Remove from oven & let it sit for a few minutes before serving. Enjoy!


*To make breadcrumbs from leftover bread, toast slices in a 250° F oven for 10 minutes or until well toasted & dry. Pulse in food processor or mortar & pestle until crumbs are the consistency you would like.
Find my Magic Tahini Seed Bread: HERE
Also see: 16 Best Substitutes for Milk in Mac and Cheese.
Also see: Sides for Mac and Cheese.


Serving: 1bowl | Calories: 638kcal | Carbohydrates: 68g | Protein: 24g | Fat: 31g | Saturated Fat: 19g | Cholesterol: 86mg | Sodium: 563mg | Potassium: 347mg | Fiber: 4g | Sugar: 3g | Vitamin A: 8423IU | Vitamin C: 15mg | Calcium: 513mg | Iron: 2mg