Healthy Baked Macaroni and Cheese

Healthy Baked Macaroni and Cheese is the perfect side dish for holidays or summer BBQs. Made with whole wheat pasta and a lightened melty cheese sauce.

When it comes to special occasions we all have our favorite Side Dishes that we just have to serve. However, there are lots healthier versions of your favorites that you can try. Between Healthy Macaroni Salad, Brussels Sprouts Gratin, Green Bean Casserole, and this Mac and Cheese recipe, you’ll have a whole list to choose from for your next holiday.

Healthy Baked Macaroni and Cheese in ramekin

The next time your family wants their favorite comfort food, try out a lighter version of homemade Macaroni and Cheese. You still get pasta smothered in a creamy cheese sauce, but it’s way healthier!

When it comes to healthy comfort foods, this Whole Wheat Macaroni and Cheese is sure to become one of your go-to recipes. The cheese casserole is great to serve for the holidays or as an easy side to go with your weeknight meal. The blend of creamy sauce and tender noodles is the perfect simple, crowd-pleasing dish to serve alongside BBQ Chicken or Pot Roast.

The recipe is also easy enough you could make it for a lunch. Some people like to double up the recipe. That way, there’s plenty to serve for dinner, but then more leftovers for to reheat for an easy and delicious lunch.

Healthy Baked Macaroni and Cheese collage

Healthy Side Dish Recipes 

Making Mac and Cheese Healthy 

Mac and Cheese is a favorite with kids and adults alike. However, between the pasta and thick, creamy sauce, it’s also quite heavy. With a few easy changes, this version is a healthier comfort food that’s still just as delicious.

The most obvious change was using whole wheat pasta for a more nutrient-rich dish. Along with using whole wheat pasta, there are a few changes to the sauce so that you can enjoy the perfect cheese sauce without all the fat and calories. Firstly, decrease the butter and the amount of cheese you’d usually find in this recipe. Second, use 2% milk instead of a heavier cream base, and finally low-fat cottage cheese is used to further thicken the sauce so it’s still rich.

You still get the same amazing cheese flavor, but with a lot less unhealthy ingredients. It’s a great way to satisfy your cheese cravings without blowing your healthy goals!

Healthy Baked Macaroni and Cheese in baking dish

Variations on Mac and Cheese 

  • Pasta: If you don’t have elbow pasta, you can try any kind of short-cut pasta. Shell, bowtie, penne, or rigatoni would all work well in this recipe.
  • Cheese: You can try different kinds of cheeses to add to or replace the cheddar cheese. If you just want a slightly stronger flavor, use extra-sharp cheddar cheese. For bigger changes, try your favorite cheeses like Parmesan cheese, Mozzarella, Swiss, Pepper Jack, Colby Jack, or Mexican blend cheese.
  • Gluten-Free: To make your Healthy Mac and Cheese gluten-free, you’ll need to replace the flour and noodles. You should be able to find gluten-free pasta at your local grocery store. For gluten-free flour, try buckwheat flour, almond flour, or oat flour.
  • Vegetables: For some extra nutrients and flavors in your casserole, add your favorite veggies to the mix. Broccoli, red onion, bell pepper, or peas would all taste amazing.
  • Toppings: You can sprinkle on some toppings before baking like shredded Parmesan, panko bread crumbs, or bacon bits.
  • Spicy: For a spicy take on the comfort food dish, try adding a dash of hot sauce or topping it off with sliced jalape√Īo pepper.
  • Chicken: To add some protein and make this a main dish, stir in cooked and diced chicken breast. Mix the chicken into the sauce along with the pasta, then bake as normal. You can also boil the noodles in chicken broth instead of water for some extra flavor.

Healthy Baked Macaroni and Cheese in baking dish

More Pasta Recipes 

How to Store Healthy Baked Macaroni and Cheese 

  • Serve: After cooking, don’t leave your Healthy Mac & Cheese out at room temperature for more than 2 hours.
  • Store: You can cover the dish in foil or plastic wrap to store it in the refrigerator for 3-5 days.
  • Freeze: Seal and freeze the recipe for up to 10 months. When you’re ready to eat it, take the dish from the freezer and let it thaw in the fridge overnight. Then reheat it for 10-15 minutes in the oven until the cheese is bubbling.

Healthy Baked Macaroni and Cheese in ramekin

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Healthy Baked Macaroni and Cheese

Healthy Baked Macaroni and Cheese is the perfect side dish for holidays or summer BBQs made with whole wheat pasta and a lightened melty cheese sauce.
Yield 10 Servings
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Course Side Dish
Cuisine American


  • 8 ounces whole wheat large elbow macaroni
  • 2 cups 2% milk
  • 2 tablespoons unsalted butter
  • 3 tablespoons flour
  • 2 cups sharp cheddar cheese , freshly shredded, divided
  • 1 cup low-fat cottage cheese , pureed
  • 1/2 teaspoon kosher salt
  • 1/2 teaspoon ground mustard
  • 1/4 teaspoon coarse ground black pepper , or ground white pepper


  • Preheat oven to 400 degrees and spray an 8x8" baking dish with vegetable oil spray.
  • In a large pot boil the pasta for 5 minutes then drain and set aside.
  • In that pot, wipe it dry with a paper towel.
  • On medium-high heat melt the butter and whisk in the flour until the flour is completely mixed in.
  • Add in the milk slowly whisking as you pour.
  • Cook, stirring constantly, for 5-6 minutes until the sauce starts to thicken.
  • Add in 1 ½ cups of the cheddar cheese and the cottage cheese whisking well.
  • Add salt, mustard, pepper, and the cooked pasta and stir to combine.
  • Pour mixture into baking dish.
  • Bake, uncovered for 25-30 minutes or until golden brown and bubbly.


Calories: 239kcal | Carbohydrates: 22g | Protein: 14g | Fat: 11g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 1g | Cholesterol: 34mg | Sodium: 373mg | Potassium: 161mg | Fiber: 1g | Sugar: 3g | Vitamin A: 354IU | Vitamin C: 1mg | Calcium: 244mg | Iron: 1mg
Keyword: Healthy Baked Macaroni and Cheese

Healthy Baked Macaroni and Cheese collage

About the Author: Sabrina Snyder

Sabrina is a trained professional chef who has cooked for private clients for over a dozen years. Experienced in handling dietary restrictions, allergies and picky kid eaters, she's well versed in coming up with healthy, yet flavorful recipes.


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