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Gluten Free Squash Mac and Cheese

  • Author: Tessa
  • Total Time: 55 mins
  • Yield: 6 to 8 entrée servings 1x


It still has cheese and milk, but healthy gluten-free butternut squash mac and cheese gets bright color from hidden veggies in an easy cheese sauce.


  • Kosher or sea salt
  • 1 lb. gluten-free brown rice pasta, such as fusilli or penne
  • 2 oz. cream cheese
  • 2 C grated cheddar cheese
  • 1 T olive or vegetable oil (plus extra for pan)
  • 1/4 C finely chopped shallot (1) or yellow onion
  • 2 t minced garlic (about 2 cloves)
  • 1 1/2 C milk (I use equal parts whole milk and almond milk)
  • 6 C diced butternut squash, frozen or fresh
  • Ground white pepper
  • 1/2 C raw pumpkin seeds
  • 5 T finely grated parmesan cheese
  • 1/4 t dried thyme (optional)
  • 1/2 T olive oil, melted butter, or melted vegan spread


  1. Set a large pot of water over high heat and keep salt and pasta nearby. Set cream cheese and cheddar out to come closer to room temp.
  2. Heat oil over medium in medium saucepan, then add shallots and cook 3 to 5 minutes, stirring occasionally, until well browned. Keep heat low enough that shallot doesn’t burn. Add garlic and sauté another minute, until fragrant. Add milk and squash and stir to mix–the squash won’t be submerged in the milk. Raise heat to medium high and cover. Once boiling, reduce to low heat and keep covered. Stir occasionally, simmering 10 to 15 minutes, until squash is fork-tender. Remove from heat and blend slightly cooled mixture with immersion blender or a standard blender until very smooth. Combine squash puree in the saucepan with cheese, 1 1/4 teaspoon salt, and 3/4 teaspoon white pepper, stirring until cheese melts.
  3. Preheat oven to 375 degrees (F).
  4. Add 1/2 tablespoon salt to boiling water, then add pasta and stir. Maintain a moderate boil. For Trader Joe’s or Tinkyada brown rice penne or fusilli, cook 5 1/2 minutes, check for doneness, then boil up to 6 1/2 minutes until very firm but edible. Turn off heat, let pasta rest in water for 30 seconds, then drain in a colander without rinsing. Add cooked pasta to sauce and stir to combine well. Spread mac and cheese in a lightly oiled 9 by 13 inch pan or baking dish.
  5. Pulse pumpkin seeds in food processor 20 to 25 times to form coarse crumbs. Combine crumbs with parmesan, thyme, salt and pepper to taste, and olive oil or melted butter, using your fingers to work fat into the crumble. Sprinkle topping over mac and cheese. Bake 15 to 20 minutes, until mac and cheese is hot and crumb topping is lightly browned. If topping doesn’t brown, broil for a minute or two. Cool slightly before serving.


If you plan to serve the mac and cheese with salsa, pesto, or other condiments, or with veggies mixed in, try omitting thyme from the crumb topping for a more basic, adaptable flavor profile.

Recipe adapted from Ashley McLaughlin of Edible Perspective, via Craftsy.

  • Prep Time: 35 mins
  • Cook Time: 20 mins
  • Category: Pasta
  • Cuisine: Gluten-Free