Healthy Baked Mac and Cheese with Pumpkin

4.56 stars average

A healthy twist on the comfort food classic, your entire family will love this baked mac and cheese with pumpkin.

Prep Time20 minutes
Cook Time25 minutes
Total Time45 minutes

Serving baked mac and cheese

A healthy twist on the comfort food classic, your entire family will love this baked mac and cheese with pumpkin.

Serving baked mac and cheese

Mac and cheese is a delicious go-to in our house, and adding in the seasonal flavor of pumpkin is a huge crowd pleaser; especially with the kids! It is the best of both worlds: it satisfies your craving for warm and hearty comfort food, but doesn’t leave you feeling like you just ate two sticks of butter.

What Makes it Healthy?

  • Eliminate White Pasta: By using whole wheat pasta instead of bleached white-flour pasta, you not only add vitamins and nutrients, but you incorporate protein and fiber which helps keep you satisfied.
  • Boost Nutrition with Pumpkin: Pure pumpkin not only adds a delicious, creamy texture, but it is a low-calorie source of vitamins including vitamin A, potassium, vitamin C, iron, and folate.
  • Swap Out Butter for Olive Oil: Do you see that gorgeous, deep brown crust on that baby? Traditionally, that is created by adding butter to the top of the bread crumbs before baking. Well, guess what? Olive oil accomplishes the same goal without the saturated fat and bad cholesterol that comes with butter. Added bonus: olive oil is a source of omega-3 fatty acids that actually lower cholesterol.

How to Make Healthy Baked Mac and Cheese with Pumpkin

pasta entering boiling pot of water

Start by cooking your pasta. I like to use elbows, but any spiral shaped pasta works great to catch the creamy sauce.

Pasta set aside in colander

Once your pasta is finished cooking, strain and set aside.

person making a roux

Next, you’ll create a nice roux in a large pot by melting your butter and mixing in the flour over medium-high heat.

Adding milk to roux

Slowly add your milk, while continuously whisking, until it begins to thicken. Typically about 5-7 minutes.

Liz adding cheese to cheese sauce.

Next, add your shredded cheese and stir in until it’s melted.

Adding pumpkin to cheese sauce

Once the cheese is melted, stir in your pure pumpkin purée for added creamy, fall flavor.

person grating garlic

Then you’ll add your grated garlic, nutmeg, salt, and pepper. As always, I like to use freshly grated ingredients using my microplane.

Stirring in pasta

Next you’ll grab the pasta you set aside and stir it into the sauce.

Adding yogurt to mac and cheese

We don’t want the mac and cheese to dry out in the oven, so adding the yogurt helps by bringing additional moisture and creaminess.

Adding dijon to pasta

You’ll top it off with your Dijon mustard, and make sure it is all mixed in and coated thoroughly.

Healthy mac and cheese before the oven

Transfer your mac and cheese to a medium sized casserole dish and sprinkle the parmesan cheese and breadcrumbs evenly over the top.

Drizzling oil on baked mac and cheese

To help get that crust crispy and brown, finish with the olive oil before popping it in the oven at 450 degrees for 20-25 minutes.

Baked Mac and Cheese with Pumpkin

You’ll know its done with the top is browned and the edges are bubbling. Remove from the oven, serve, and enjoy!

Frequently Asked Questions:

How do I store the leftovers?

Keep it in the fridge in an airtight container for up to 4 days, or in the freezer for up to 3 months.

Can I make this mac and cheese ahead of time?

Yes of course! Prepare it up to the point of baking, but instead of popping it in the oven, cover it and put it in the fridge for up to 24 hours. If you don’t plan on baking it for a couple days, I would put it in the freezer.

Is pumpkin purée and pumpkin pie mix the same?

No, they are not. It can be confusing since they are typically found on the same shelf at most grocery stores, but make sure you are grabbing pure pumpkin purée, and not the pumpkin pie mix.

Serving healthy baked mac and cheese with pumpkin.

Easy Ingredient Swaps

Of course, changing up the ingredients will also change up the nutritional value, but here are some other healthy options if you want to shake things up.

  • Don’t have plain yogurt? You can also use low-fat sour cream or cottage cheese.
  • Swap out the pumpkin. Try it with butternut squash, broccoli, or carrots! Really any veggie can be added to this delicious baked mac and cheese.
  • Make it gluten free. You can always replace the bread crumbs with crushed corn tortilla chips, corn meal, almond flour, or crackers. And swap out the pasta for a gluten-free noodle.
  • Dairy-free mac and cheese. I know you might be thinking, dairy-free mac and cheese? But it’s totally possible to enjoy this comfort food even if you can’t have dairy. Replace the milk with plain, unflavored almond milk. Use vegan cheese; there are plenty of options that are soy or rice based. To still get the tangy, creaminess of the yogurt, use coconut milk with a squeeze of lemon juice.

Other Recipes to Try

Are you a cheese fiend? I have plenty of other delicious, cheesy recipes to try. Here are just a few to get you started:

Love all things pumpkin? Here are some other great recipes using pumpkin!

person enjoying backed mac and cheese with pumpkin

Eating healthy doesn’t mean you have to sacrifice comfort foods, and this Baked Mac and Cheese with Pumpkin is one of my favorites.

Your fork is waiting.

Serving baked mac and cheese

Healthy Baked Mac and Cheese with Pumpkin

4.56 stars average
A healthy twist on the comfort food classic, your entire family will love this baked mac and cheese with pumpkin.
PREP: 20 minutes
COOK: 25 minutes
TOTAL: 45 minutes
Servings: 6


  • 12 ounces whole wheat elbows (cooked al dente)
  • 1 tablespoon butter (unsalted)
  • 2 tablespoons flour
  • 2 cups milk (any type)
  • 1 ½ cups shredded sharp cheddar (2% reduced fat)
  • 1 cup pure pumpkin
  • 1 tablespoon dijon
  • 1 clove garlic (grated)
  • ½ teaspoon salt
  • ¼ teaspoon pepper
  • teaspoon nutmeg
  • cup plain yogurt (low fat)
  • 2 tablespoons bread crumbs
  • ¼ cup grated parmesan
  • 1 tablespoon extra virgin olive oil


  • Pre-heat oven to 450 degrees and have a medium-sized casserole dish ready. Place prepared pasta in a large bowl and set aside.
  • Melt butter in a medium sauce pot and gently whisk in flour. Slowly pour in milk and continuously whisk over medium heat until it begins to thicken, about 5-7 minutes. Stir in shredded cheese, pumpkin, grated garlic, salt, pepper, and nutmeg. Whisk mixture until cheese is melted and sauce thickens even further, about 5 more minutes.
  • Pour pumpkin cheese sauce over the pasta in the bowl and mix until pasta is evenly coated. Stir in plain yogurt and Dijon, then pour entire mixture into baking dish.
  • Sprinkle bread crumbs, parmesan, and olive oil evenly on top of the pasta then bake uncovered for 20-25 minutes until the contents bubble and the top forms a nice crust.


Calories: 366kcalCarbohydrates: 54.5gProtein: 18.3gFat: 8.7gSaturated Fat: 4gPolyunsaturated Fat: 4.7gCholesterol: 21mgSodium: 594mgFiber: 5gSugar: 2.5g

40 thoughts on “Healthy Baked Mac and Cheese with Pumpkin”

  1. Wow — this is delicious. I baked up a batch and froze individual portions to send off to college with my daughter. She love it too. Thanks so much for the recipe.

  2. I have a tried and true Mac & Cheese recipe already, but I had pinned this on Pinterest a few weeks ago and decided to look up the ingredients to see if I had everything to make it. Well…I had to make some modifications according to what I had since there’s no way I was going to the grocery store. I used regular elbow pasta, 2% milk, sour cream instead of yogurt, and sharp cheddar instead of reduced fat. I had a date with the gym after cooking, so I didn’t try any, but my fiance did when he got home from work. He really liked it! It’s way different than my regular recipe, but he liked it. He started asking me what I put in it. I made sure I told him about the pumpkin once he admitted to liking it. ;) I knew he would never suspect it! Thanks for sharing this! Got a healthy mac & cheese recipe now…well, when I have the proper ingredients that is. :)

  3. is the Dijon nessecary? my family doesn’t usually eat Dijon and I’d hate to buy it for such a small amount? or is there a spice or something else I could maybe use? thanks so much, I’m excited to make this and bring it to school to share!

  4. HI.. Little confused for me.. U jusy say — Add milk and flour to a medium sauce pot and continuously whisk over medium heat until it begins to thicken, about 5-7 minutes without any butters? It will take thick?

    1. Hi again.. I did made them yesterday — w/o butter for roux… Tastes WONDERFUL!! I am sure that I will make them again for Thanksgiving dinner with big family! Thank you so much because I trust that food for big family.. =)

  5. My husband, unfortunately, passed on his tradition of Kraft Mac & Cheese to my almost four year old (ugh) – you couldn’t pay me enough to eat that stuff! Maybe because I grew up in South Africa and never acquired a taste for it. (I don’t know if we even got it there – but I never saw it in my family!) Anyway, if I can get Mr. Picky and little Miss Picky to eat this instead I will be FOREVER grateful! Look forward to trying it – I’ll let you know how it goes!

    1. Please try it!! My husband is also very picky and HATES mac and cheese because of too much boxed stuff growing up. He devoured it and so did my 2 year old!

  6. I LOVE this recipe! I made something like this last year, but never got it quite right. I really like that you list your nutritional info and explain how you lightened up the recipe! I may do the same on my blog. Great job and beautiful work!

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