Pumpkin Mac and Cheese is creamy, dreamy, cheesy pasta love, gone deceptively light.  

Pumpkin Mac and Cheese with Bacon and Caramelized Onions

Get pumped: this outrageously decadent pasta (that you’re sure to be shoveling in your face shortly) happens to be good for you!

While I can’t promote Pumpkin 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 reasonably healthy.

We owe this double fist pump-worthy miracle to two super ingredients: pumpkin puree and my favorite healthy cooking weapon, Greek yogurt.

The pumpkin puree and the Greek yogurt add guilt-free depth and body to the sauce.

Fear not, cheese still represents—surely you know this Wisconsin resident well enough to realize I would never deny you cheese.

Sharp cheddar and Parmesan bring big cheese taste, but a little of these two flavor-jammers goes a long way.

When the gooey cheddar melts with the creamy pumpkin sauce, the pumpkin flavor mellows and the cheddar steals the spotlight.

This is macaroni and cheese after all. All is well with the world.

Pumpkin Mac and Cheese with Bacon and Caramelized Onions

We enhance our luscious pumpkin cheddar sauce with a touch of nutmeg to complement the pumpkin’s natural flavors, as well as a subtle kick of cayenne and dry mustard, just to keep everyone awake.

Now, we could leave our velvety Pumpkin Mac and Cheese as is and live happily ever after, but mac and cheese is meant to be comfort food.

Enter crispy bacon and caramelized onions to add an extra layer of flavor and richness.

Plus, adding caramelized onions to anything renders it instantly appropriate to serve at a fancy dinner party.

Do serve Pumpkin Mac and Cheese at your next fancy dinner party. A fancy dinner party with Pumpkin Mac and Cheese is wayyyyy more fun than a fancy dinner party without it.

Just ask anyone—they’ll agree. You are about to be the Hostess of the Year.

Pumpkin Mac and Cheese with Bacon and Caramelized Onions in a red baking dish

Now, let’s talk topping.

No self-respecting baked mac and cheese dish would be complete without that gloriously golden Parmesan breadcrumb crust.

I insist on being the one to dish out the Pumpkin Mac and Cheese, because I relish that first moment of crashing the serving spoon through the wondrous breadcrumb crust  to reach the creamy, saucy noodles underneath.

Plus, when I serve Pumpkin Mac and Cheese, I can strategically sneak any excess topping onto my own plate.

I call this the “cook’s privilege.”

Dive right on into a big bowl of velvety Pumpkin Mac and Cheese. Be sure to sneak yourself an extra scoop of the crusty golden topping!

Pumpkin mac and cheese in a white bowl

Pumpkin Mac and Cheese

5 from 2 votes
Pumpkin Mac and Cheese with Caramelized Onions and Bacon is comfort food light, done right. With Greek yogurt, pumpkin puree, and extra sharp cheddar, this baked pasta dish tastes completely creamy and indulgent, yet is still reasonably healthy. With a crunchy Parmesan breadcrumb topping, this baked macaroni and cheese is total perfection!

Prep: 35 mins
Cook: 55 mins
Total: 1 hr 30 mins

Servings: 4 – 6 servings


  • 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


  • If necessary, cook the bacon according to 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. 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 dish. In a small bowl, combine breadcrumbs, remaining 2 tablespoons Parmesan, and remaining 1 teaspoon olive oil. Sprinkle the mixture evenly over the noodles. Cover dish with foil and bake 20 minutes. Remove foil and continue baking until lightly browned and crisp on top, 30 to 35 minutes more. Serve immediately.


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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at wellplated.com and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. Made this today for seven people and they all loved it! The best part is that there is some left for tomorrow. thank you so much for this yummy recipe.

    1. Jonna, I am so SO excited to hear that! Thanks so much for letting me know, and I hope you enjoy the leftovers too :)

  2. I can’t wait to make this for tonight’s dinner. I love that the recipe has bacon in it. There’s nothing that can’t be made better with the addition of bacon. I will also use 4 Italian Cheese Cheez-It’s in place of the panko crumbs. There’s no such thing as too cheesy.

  3. I made this for a fall harvest party that we had two weeks ago. It was such a success that I made it again last night for family dinner. Now my mother-in-law says that I will have to bring it to Thanksgiving dinner. You don’t taste the pumpkin, it is just rich and creamy. My husband couldn’t believe it as he was originally adamant about not wanting pumpkin in his mac and cheese. It is amazing, thank you so much for the wonderful recipe.

    1. Rebecca, I can’t tell you how happy this comment makes me! I would be honored if this dish became a part of your Thanksgiving dinner, and I’m so glad that you and your family enjoyed it. Thanks for letting me know, and have a great day!

  4. 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! I used 2% milk instead of skim, and I didn’t have any panko so I left it out, but this was still such a delicious meal! My husband and I both feel that this would be an awesome dish served with fried chicken (although that would defeat the purpose of this being a healthy dish LOL)! I served it with a side of broccoli and it was a great meal. Thanks sooooo much for your awesome healthy dinner recipes. I am such a huge fan of yours and check your website all the time!

  5. My mom and I made this for my birthday dinner! (Sans the bacon, I’m not a fan of bacon.) My dad thought it was weird, but my older sister, mother and I absolutely loved it! The pumpkin added a squash-y flavor, not a sweet one like my mom initially expected when I showed her the recipe. I absolutely love everything I’ve made from this site so far and I’ll continue using it to encourage my family to eat healthier. Oh! And, the amount of cheese wasn’t too much, either. Using too much cheese makes things greasy, in my opinion, so I’m glad that it wasn’t greasy.5 stars

  6. Do you have the nutritional information for this recipe available? It sounds delicious, but I’m on a strict diet due to serious illness and need to know nutritional information before I cook something. Thanks!

    1. Hi Lauren! I started adding nutrition info in 2016, and unfortunately it’s too time consuming to go back and add it to recipes published before that. If you’re interested, an online calculator like MyFitnessPal may be a helpful resource. I hope this helps!

  7. Sounds delish!  Only concern I have is the pasta itself.  We are eating a keto based diet and I’m Thinking I could likely sub out the Pasta for cauliflower crumble instead?  Has anyone tried it that way?  Also using heavy cream instead of milk?  

    1. Hi LeanneKen! I haven’t tried this swap, so I’m not sure how it might turn out. If you decide to experiment, I’d love to hear how it goes!

  8. Our family absolutely LOVED this recipe! I have now made so many of your recipes, and my family loves them all! I’m definitely serving this pumpkin mac and cheese as a side for Thanksgiving! I substituted turkey bacon for bacon, and it was absolutely delicious! I also doubled the parmesan breadcrumb topping. Thank you so much for this amazing recipe!5 stars

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