Pumpkin Mac and Cheese {with Healthy Greek Yogurt} – WellPlated.com

Pumpkin Mac and Cheese is creamy, dreamy, cheesy pasta love, gone deceptively light (and ultra-festive for fall and the holidays too).  

a bowl of creamy pumpkin mac and cheese

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Get pumped: there’s a new mac and cheese recipe in town, and it’s everything you want (and more) in this famous comfort food classic.

This is pumpkin mac and cheese, and it’s going to be the star at your next holiday gathering or dinner party.

a casserole dish with pumpkin mac and cheese

5 Star Review

“I just found this recipe a couple days ago and I made it last night and it was so good!! My family totally loved it! ”

— Sharice —

While I can’t promote pumpkin mac and cheese (or Adult Mac and Cheese) as a health food per se, you will be hard-pressed to find another healthy mac and cheese recipe that tastes this rich, while actually being a reasonably healthier option (this Tuscan Chicken Mac and Cheese is a close second).

We owe this cheesy miracle to two super ingredients: pumpkin puree and my favorite healthy cooking weapon, Greek yogurt.

  • The pumpkin puree adds fiber, iron, vitamin A, and a luscious, smooth texture.
  • While the Greek yogurt adds guilt-free depth, body, and creaminess to the sauce.
a close up shot of tasty pumpkin mac and cheese with bacon and breadcrumbs

Fear not, cheese still represents here—a blend of sharp cheddar and Parmesan brings a big cheese taste that mellows the pumpkin flavor so it isn’t too overpowering (we’ll save the BIG pumpkin flavor for this Healthy Pumpkin Bread).

This is macaroni and cheese after all.

How to Make Pumpkin Mac and Cheese

Tender pasta cooked in a velvety smooth homemade pumpkin cheddar sauce is speckled with caramelized onions, crisp smoky bacon, and a touch of spice before being finished with a crunchy Parmesan-panko topping.

a bowl with the best pumpkin mac and cheese

The Ingredients

  • Macaroni. Classic elbow macaroni is my go-to pasta style for this healthy pumpkin mac and cheese. I typically opt for whole wheat pasta to sneak in some whole grains too.

Substitution Tip!

Any short-cut pasta will work for this recipe. Rigatoni, penne, or rotini are all great options. Trader Joe’s often has adorable pumpkin-shaped pasta in the fall to make this a fun pumpkin mac and cheese for toddlers and kids (kids love this Spicy Pizza Mac and Cheese too).

  • Pumpkin Puree. Rich in fiber, vitamin A, and other nutritious vitamins, minerals and antioxidants, pumpkin turns everyday mac and cheese into a superfood (I love it for this Alfredo-style Pumpkin Pasta Sauce too).
  • Bacon. Even healthy mac and cheese needs a liiiiittle bacon. You can of course omit it if you want to trim the fat and calories further.
  • Onion. Sweet caramelized onions complement the sweetness of the pumpkin and the smokiness of the crisp bacon.


Let your onions continue to caramelize on low heat while you prepare the rest of the mac and cheese components. You double your productivity, and the longer the onions cook, the sweeter they become.

a casserole dish with healthy pumpkin mac and cheese
  • Low-fat Milk + Chicken Broth. Makes the sauce creamy without feeling heavy.
  • Greek Yogurt. My secret ingredient for making a “healthy” mac and cheese that’s lower in fat and calories while still tasting rich and creamy.


While I’m usually all for nonfat Greek yogurt in my recipes (as in these Healthy Pumpkin Muffins), I like to use a yogurt with at least a little fat in this recipe to give the sauce a bit of richness. It is also less prone to curdling.

  • Spices. A blend of mustard powder, nutmeg, and cayenne gives the sauce depth of flavor.
  • Cheddar Cheese. I recommend using sharp cheddar for max flavor impact. You don’t need as much to create a bold, cheesy taste.
  • Parmesan Cheese. Tastes heavenly when sprinkled on top and toasted in the oven with the panko.


Feel free to try other blends of cheese in this pumpkin mac and cheese recipe. When selecting cheese, choose varieties that are aged or have a sharp flavor for best results. Gruyere, Aged Gouda, Emmental, Asiago, or Romano would all be suitable alternatives.

  • Panko Breadcrumbs. Creates an insanely crunchy crust that blankets the cheesy, pumpkin pasta as it bakes in the oven.

The Directions

  1. Cook the bacon.
sliced onions in a skillet
  1. Saute the onions until softened.
sautéing onions in a skillet
  1. Continue to cook onions until caramelized.
stirring pumpkin puree into milk and broth
  1. Simmer the pumpkin, stock, and milk until thickened.
creamy homemade pumpkin pasta sauce for macaroni and cheese
  1. Season with mustard, salt, pepper nutmeg, and cayenne.
Stirring cheese, Greek yogurt, and pumpkin sauce into cooked pasta for pumpkin mac and cheese
  1. Cook the pasta till al dente. Drain, then pour pumpkin sauce over the top and stir in the cheese and Greek yogurt.
stirring sautéed onions into pumpkin macaroni and cheese in a glass bowl
  1. Fold in all of the caramelized onions and reserved bacon.
A casserole dish of healthy pumpkin mac and cheese ready to be baked
  1. Transfer to a greased casserole dish. Top with breadcrumbs, Parmesan, and a drizzle of olive oil.
  2. Bake until lightly browned and crisp on top. Serve immediately and ENJOY!

Dietary Note

If you’re wondering how to make pumpkin mac and cheese vegan, here are my tips to adapt the recipe (if you try it, I’d love to hear how it goes!):

  • Substitute the milk for your favorite dairy-free milk.
  • Swap the Greek yogurt for either soy, almond, or coconut milk yogurt.
  • Opt for cheddar-style vegan cheese shreds.
  • Choose vegetable stock instead of chicken stock.
  • Omit the bacon or fold in a vegan bacon of your choice.

Storage Tips

  • To Store. Leftover pumpkin mac and cheese may be stored in a covered airtight container in the fridge for up to 3 days.
  • To Reheat. Warm pumpkin mac and cheese in the microwave, covered, until steaming. Alternatively, you may rewarm the mac and cheese in a 350 degree F oven until heated through.

Meal Prep Tip

Make room for pumpkin mac and cheese on your holiday menu with these meal prep tips for make-ahead pumpkin mac and cheese. It’s an easy, low-fuss side dish to add to your spread.

  • Grate your cheese, cook your bacon, caramelize the onions, and toss together your breadcrumb mixture up to 1 day ahead. Store in individual containers in the refrigerator.
  • Precook the macaroni up to 1 day ahead. Drain, drizzle with a little olive oil (prevents the noodles from sticking together), and then store in an airtight container in the fridge until ready to use.
  • Prepare the sauce as directed, let cool completely, then store in an airtight container in the fridge up to 1 day ahead.
  • When ready to cook, fold together the cooked pasta, pumpkin sauce, cheese, onions, and bacon. Then transfer to a casserole dish and top with breadcrumbs. Bake as directed.

What to Serve with Pumpkin Mac and Cheese

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Recommended Tools to Make this Recipe

  • Pasta Pot. Makes it easy to boil and drain your perfectly cooked al dente pasta.
  • Casserole Dish. This beautiful Le Creuset dish will be the centerpiece on your table.
  • Mixing Bowls. This durable, everyday set of dishwasher-safe glass mixing bowls should be in everyone’s kitchen.

The Best Pasta Pot

This 12-quart Cuisinart pasta pot and steamer has an aluminum base for even heat distribution, plus a stainless steel inside surface perfect for not discoloring or altering flavors.

a bowl of creamy pumpkin mac and cheese

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Frequently Asked Questions

Does Pumpkin Mac and Cheese Taste Like Pumpkin?

It depends. Some pumpkin mac and cheese recipes go heavy on the cheese and spices which can often mask the slightly sweet squash flavor of the pumpkin. Others let the pumpkin really shine. In this recipe, the pumpkin flavor is quite mild and is complemented by the nutmeg and touch of cayenne.

Is Pumpkin Mac and Cheese Healthy?

Relative to other mac and cheese options, this particular recipe is healthier than most thanks to Greek yogurt and plenty of pumpkin puree. With that being said, I would not consider pumpkin mac and cheese to healthy in the same way I would consider this Kale and Brussels Sprouts Salad to be healthy.

Can I Use Pumpkin Pie Filling Instead of Pumpkin Puree?

No. When a recipe calls for pumpkin puree, you cannot substitute pumpkin pie filling. Pumpkin pie filling contains a lot of added sugars, spices, and other stabilizing ingredients that would affect both the taste and texture of this pumpkin mac and cheese.

  • 4 ounces bacon cooked (4–5 pieces)*
  • 3 teaspoons  extra-virgin olive oil divided
  • 2 cups yellow onion thinly sliced (about 1 large)
  • 1 can pumpkin puree (not pumpkin pie filling) (15 ounces)
  • 1 1/2 cups nonfat milk
  • 1 cup low-sodium canned chicken stock (if homemade, skim off fat)
  • 1 teaspoon dry mustard
  • 3/4 teaspoon kosher salt
  • 1/4 teaspoon black pepper
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon cayenne pepper
  • 13 ounces whole wheat elbow macaroni or other short pasta, such as penne or rigatoni
  • 4 ounces extra-sharp cheddar cheese, finely grated (about 1 cup)
  • 1/3 cup 2% plain Greek yogurt (I use Chobani)
  • 1 ounce Parmesan cheese, finely grated (about 1/4 cup), divided
  • 1/4 cup panko breadcrumbs

  • Cook the bacon until crisp (try one of my easy methods listed below). Once cool enough to handle, chop into rough pieces and set aside.

  • Preheat the oven to 350 degrees F. In a large skillet, heat 2 teaspoons olive oil over medium-high heat. Add onions and sauté just beginning to soften; about 3 minutes.

  • Reduce heat to medium-low and continue to cook onions until caramelized and tender, stirring occasionally. Let the onions cook for at least 10 additional minutes, or up to 30 minutes as you prepare the rest of the recipe.

  • In a deep, wide saucepan, combine pumpkin, stock, and milk, then bring to a boil over medium-high heat. Reduce heat to medium and simmer until sauce thickens slightly; about 8 minutes.

  • Remove from heat, then stir in mustard, salt, pepper nutmeg, and cayenne.

  • Meanwhile, bring a large pot of water to a boil. Add noodles and 1 tablespoon kosher salt, then cook just until al dente according to package instructions. Drain, then transfer noodles to a large bowl. Pour pumpkin sauce over the top, then stir in the cheddar, Greek yogurt, and 2 tablespoons Parmesan.

  • Fold in all of the caramelized onions and reserved bacon.

  • Lightly coat a 9-inch square, deep baking dish or a 2-quart casserole dish with cooking spray. Transfer the pumpkin noodle mixture to the dish. In a small bowl, combine breadcrumbs, the remaining 2 tablespoons Parmesan, and the remaining 1 teaspoon olive oil. Sprinkle the mixture evenly over the noodles.

  • Cover dish with foil and bake for 20 minutes. Remove foil and continue baking until lightly browned and crisp on top; 30 to 35 minutes more. Serve immediately.

  • *Easy bacon cooking methods: Oven Baked Bacon or Air Fryer Bacon.
  • TO STORE: Leftover pumpkin mac and cheese may be stored in a covered airtight container in the fridge for up to 3 days.
  • TO REHEAT: Warm pumpkin mac and cheese in the microwave, covered, until steaming. Alternatively, you may rewarm the mac and cheese in a 350 degree F oven until heated through.

Serving: 1(of 6)Calories: 500kcalCarbohydrates: 63gProtein: 24gFat: 19gSaturated Fat: 8gPolyunsaturated Fat: 2gMonounsaturated Fat: 8gTrans Fat: 1gCholesterol: 37mgPotassium: 571mgFiber: 3gSugar: 8gVitamin A: 11401IUVitamin C: 7mgCalcium: 343mgIron: 4mg

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