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Butternut Squash Mac and Cheese Cupcakes

Butternut Squash Mac and Cheese Cupcakes

When I told my son that we were having noodle cupcakes for lunch, he was super excited:  “Noodle cupcakes!!  Noodle cupcakes!!” he repeated again and again.  All noodles are the same to my son at this point (there is one exception to this, which I’ll detail below), so I didn’t bother specifying that they were butternut squash mac and cheese cupcakes.

Since my son helped me prepare the mac and cheese cupcakes, he knew that they were actually butternut squash mac and cheese cupcakes.  He loves squash of all kinds, so this is a plus for him.  Non-squash eaters, however, can safely be left ignorant of the vegetable’s presence in the cupcakes.  If you don’t tell tasters that there are 20 ounces of butternut squash in the recipe, they would never know it – it blends into the mac and cheese completely.

The butternut squash mac and cheese cupcakes are wonderful to eat just out of the oven.  You’ll need to use a fork as you are still dealing with hot, melty cheese.  They are also surprisingly good cold.  If you serve them straight from the refrigerator, they become a snacky finger food (like a cupcake).  Most of us are not used to eating noodles cold; just think of the noodles as any other starch – imagine “bread and cheese” or “cheese and crackers” or, for the college students out there, “cold pizza” – and take a bite.

Butternut Squash Mac and Cheese Recipe

I got the recipe for the butternut squash mac and cheese by adapting a butternut squash mac and cheese recipe made by Brynn of WikiKitchen (she adapted it from Ellie Krieger of the Food Network).  Brynn entered a contest on the Cupcake Project Facebook page to have one of her recipes turned into a savory cupcake.  She won!  Brynn is a college student and she calls WikiKitchen a place where “college students and other busy people can find quick and healthy recipes.”  Brynn is also a Trader Joe’s junkie.  If you regularly shop there, you’ll enjoy reading her recipes that call out ingredients purchased there.

Brynn’s version of butternut squash mac and cheese used whole wheat pasta.  She explains in detail in her post why that is the healthy choice.  I would have used whole wheat pasta, but when I mentioned above that there is one kind of pasta my son doesn’t like – well, it’s whole wheat.  I’m not done trying to serve it to him, but I thought I’d stick with the classic white pasta for this recipe.  The other changes that I made to her recipe include removing the peas (I thought about replacing them with bacon.  I didn’t, but someone should try it; it would be delicious.), switching the cheese to a smoked Fontina, and turning the recipe into cupcakes!

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5 from 2 votes

Butternut Squash Mac and Cheese Cupcakes

Individual "cupcakes" of macaroni and cheese, enhanced with butternut squash.
Course Main Course
Cuisine American
Keyword butternut squash macaroni and cheese, macaroni and cheese cupcakes
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Servings 10 jumbo cupcakes or 20 regular cupcakes
Calories 418kcal
Author Stef


  • 1 pound elbow macaroni
  • 20 ounces butternut squash I went the lazy route and bought the frozen pre-cubed stuff.
  • 2 cups milk Any milk will do. I used soy milk. Whole milk would probably taste the best.
  • 2 cups grated soft cheese I went with a smoked Fontina that I had to grate myself. Obviously, it would be much easier to buy a bag of pre-grated cheese.
  • 1/2 cup ricotta cheese
  • 1/4 teaspoon salt
  • 1 teaspoon dry mustard
  • 1/4 teaspoon cayenne pepper
  • 4 garlic cloves minced
  • 1/2 cup diced onion
  • 1 cup grated hard cheese I used a mix of Parmesan, Romano, and Asiago.
  • 1 cup Panko breadcrumbs To play up the cupcake nature of this mac and cheese, you could color the panko as I did in my post on panko sprinkles.
  • 1/2 teaspoon olive oil


  • Cook the macaroni according to the package instructions. Don't overcook it. It should be tender, but firm (5-8 minutes).
  • Drain the macaroni and transfer it to a large bowl.
  • Place the squash and milk in a large saucepan and cook over medium heat. Stir occasionally and bring to a boil.
  • Transfer to a blender or food processor and combine until smooth.
  • Transfer back to saucepan and stir with grated soft cheese and ricotta until the cheeses are all melted.
  • Remove from heat and add salt, mustard, and cayenne pepper.
  • Pour cheese mixture over the macaroni and stir to combine.
  • Mix in the garlic and onions.
  • Fill cupcake liners with the mixture. Because this is mac and cheese and not cupcake batter, you don't need to worry about the mixture rising. Don't be afraid to fill the liners in a heaping mound. The mac and cheese cupcakes will look more fun that way.
  • In a small bowl, combine grated hard cheese, panko breadcrumbs, and oil.
  • Sprinkle mixture over the top of the mac and cheese cupcakes.
  • Bake at 375 F for 20 minutes or until topping is lightly browned.


Nutrition Facts
Butternut Squash Mac and Cheese Cupcakes
Amount Per Serving
Calories 418 Calories from Fat 135
% Daily Value*
Fat 15g23%
Saturated Fat 8g40%
Cholesterol 48mg16%
Sodium 510mg21%
Potassium 432mg12%
Carbohydrates 49g16%
Fiber 3g12%
Sugar 6g7%
Protein 20g40%
Vitamin A 6500IU130%
Vitamin C 12.9mg16%
Calcium 396mg40%
Iron 1.5mg8%
* Percent Daily Values are based on a 2000 calorie diet.
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