RecipeButternut Squash Mac and Cheese Muffins

Nutrition Facts
Amount per Serving
  • Calories: 110
  • Protein: 7 g
  • Total Fat: 3 g
    • Unsaturated Fat: 1.5 g
    • Saturated Fat: 1.5 g
  • Cholesterol: 10 mg
  • Total Carbohydrate: 17 g
  • Dietary Fiber: 1 g
  • Total Sugar: 2 g
    • Natural Sugar: 2 g
    • Added Sugar: 0 g
  • Sodium: 135 mg

Build me up…butternut squash cups of mac and cheese! These love muffins are so GOOD and come jam-packed with nutrition. That’s because I sneak in bright and beautiful butternut squash, which camouflages perfectly into the velvety cheddar cheese. In fact, if you have picky eaters in the house, they’ll never know veggies are hidden inside. Time-saving recipe shortcut: use canned sweet potato, butternut squash, or yam purée and skip the roasting step completely. You can opt for any elbows you like—whole grain, gluten-free, legume-based, etc.—the pasta-bilities are endless. And while you may decide to dig into the pot before the mac and cheese makes it to the muffin tin (no judgment here, been there a few times!), there’s great fun in serving them as muffins, too. I mean, indulgent mac and cheese that’s good for you and you can eat with your hands—it doesn’t get better than that!

If you’d rather go the traditional casserole route, try this recipe.


  • Prep time
  • Total Time
This recipe makes 22 muffins
  • • 5 to 6 cups cubed butternut squash or sweet potato *
  • • ½ teaspoon kosher salt, divided
  • • 1 box (14 to 16 ounces) whole-grain elbow macaroni
  • • 1 cup low-fat milk (skim, 1% or 2%)
  • • ½ teaspoon onion powder
  • • ¼ teaspoon dry mustard
  • • ⅛ teaspoon paprika
  • • ⅛ teaspoon black pepper
  • • A few drops hot sauce, optional
  • • 2 cups shredded 2% sharp cheddar cheese
  • • 1 tablespoon butter, softened
  • • 1 large egg, lightly beaten
  • • ¼ to ½ cup grated Parmesan for sprinkling on top

*Can swap with 1 cup canned sweet potato, butternut squash, or yam purée.


Preheat oven to 400˚. Mist 2 standard muffin tins with nonstick oil spray and set aside.

Mist a baking sheet with oil spray and add the butternut squash. Mist the tops of squash with additional oil spray and sprinkle with ¼ teaspoon kosher salt. Roast in oven for about 20 to 25 minutes, or until squash is super soft and fork tender. Allow to cool. Then, using a fork, mash the cubes on the baking sheet until they’re the consistency of mashed potatoes. Set aside. Reduce oven temperature to 350˚.

While butternut squash bakes, prepare the pasta and cheese sauce: Bring a large pot of water to a boil. Add the macaroni and follow the directions on the package for al dente pasta (about 6 to 7 minutes). Drain and return to pot.

In a large saucepan, combine the milk with onion powder, dry mustard, paprika, remaining ¼ teaspoon kosher salt, black pepper, and optional hot sauce. Place over medium heat, and cook until the mixture comes to a gentle simmer. Then, turn off the heat so the milk doesn’t curdle. Add the shredded cheese and stir until melted and velvety. Add the butternut squash puree and butter, stirring until completely combined. (It’s okay if there are some small squash pieces throughout)

Add the sauce to the cooked macaroni and stir until everything is evenly coated. Stir in the egg and mix well (the egg helps the muffins to hold their shape).

Split the mixture among the prepared muffin tins (about ½ cup in each, you will make ~22 muffins), pressing down to pack the compartments. Sprinkle Parmesan over the tops. Bake in the oven for about 20 minutes or until tops are slightly browned. Remove and allow to cool for 5 to 10 minutes so muffins can firm before serving (It’s important to let them sit so they don’t fall apart). Remove from muffin tin by sliding a spoon around the inside edges to prevent breakage.

Note: You can freeze muffins for future meals. While they will stay intact when defrosted and warmed in the microwave, they become more fragile and tend to lose their shape when eaten. They are still super tasty and offer the same fun presentation, but don’t stay together as they do when first cooked.

Makes 22 muffins; 1 muffin per serving


Try my Penne alla Vodka or Butternut Squash Mac and Cheese casserole.