Healthy Baked Mac Cheese

Section: Cozy Meals for Every Mood

This comforting dish combines whole wheat elbow macaroni with a velvety sauce made from sharp cheddar, mozzarella, and Greek yogurt. Flavored with Dijon mustard, garlic, and onion powders, the sauce is poured over perfectly cooked pasta and topped with crispy whole wheat breadcrumbs for texture. Baking results in a golden, bubbly finish, delivering a balanced meal that is both hearty and nourishing. Optional additions like steamed cauliflower puree and vegetables can enrich the dish further.

Harper
Contributed by Harper
Last updated on Thu, 02 Oct 2025 23:12:47 GMT
A bowl of baked mac and cheese with a sprig of parsley on top. Save
A bowl of baked mac and cheese with a sprig of parsley on top. | flavorrhaven.com

This healthy baked mac and cheese offers all the comforting creaminess of the classic dish but with a nutritious twist. It's perfect for anyone wanting a family-friendly meal that sneaks in vegetables and uses wholesome ingredients without sacrificing flavor or satisfaction.

I first made this when trying to find a healthier spin on a favorite childhood comfort food. It quickly became a go-to because even my picky eaters asked for seconds.

Ingredients

  • Whole wheat elbow macaroni or high-protein pasta: for added fiber and sustained energy
  • Low-fat milk or unsweetened almond milk: as a lighter dairy option that keeps the sauce creamy
  • All-purpose or whole wheat flour: to thicken the sauce without heaviness
  • Plain Greek yogurt nonfat or low-fat: adds tangy richness and boosts protein
  • Sharp cheddar cheese: for strong flavor
  • Part-skim mozzarella cheese: melts beautifully and keeps the dish lighter
  • Dijon mustard: balances the cheese with a subtle zing
  • Garlic powder and onion powder: provide depth of flavor
  • Salt and black pepper: for seasoning, adjust to taste
  • Whole wheat breadcrumbs or crushed almonds: for a crunchy topping
  • Olive oil or melted butter: to mix into the topping and help it brown nicely
  • Optional steamed cauliflower puree: to enrich the sauce with hidden vegetables and creaminess
  • Optional add-ins like steamed broccoli, spinach, peas, or cooked chicken: to customize the dish

Instructions

Preheat the Oven:
Set your oven to 375 degrees Fahrenheit (190 degrees Celsius) and lightly grease a 9 by 9-inch baking dish or a similar sized casserole dish. This ensures the mac and cheese won't stick and will bake evenly.
Cook the Pasta:
Bring a large pot of salted water to a boil and cook the pasta according to the package directions until it is al dente, meaning it is tender but still has a slight firmness when bitten. Drain thoroughly and set aside so it does not overcook.
Make the Roux and Sauce:
In a medium saucepan over medium heat, whisk together the flour and milk until completely smooth. Continue cooking for about three to four minutes. This process thickens the milk into a creamy base without lumps.
Add Cheese and Seasonings:
Lower the heat to low and stir in the Greek yogurt, sharp cheddar, mozzarella, Dijon mustard, garlic powder, onion powder, salt, and pepper. Stir continuously until all the cheese has melted and the sauce becomes smooth and creamy. If you choose to use steamed cauliflower puree, fold it in at this stage to create an extra nutrient-rich sauce.
Combine Pasta and Sauce:
Pour the cheese sauce over the cooked pasta in a large bowl. Mix gently but thoroughly so every piece of macaroni is coated evenly with the creamy sauce.
Transfer to Baking Dish:
Spoon the cheesy pasta mixture into your prepared baking dish, spreading it out evenly so it bakes uniformly.
Prepare and Add the Topping:
Combine the whole wheat breadcrumbs or crushed almonds with olive oil or melted butter in a small bowl. This mixture will form a crispy, flavorful topping. Sprinkle it evenly over the top of the pasta.
Bake:
Place the dish in the preheated oven and bake uncovered for about 20 to 25 minutes. The topping should turn golden brown and the sauce will be bubbly around the edges.
Cool and Serve:
Allow the baked mac and cheese to cool slightly before serving. This resting time helps the sauce thicken and improves the texture for the best comfort food experience.
A close up of a baked mac and cheese dish.
A close up of a baked mac and cheese dish. | flavorrhaven.com

Store leftovers in an airtight container in the refrigerator for up to four days. Reheat gently in the microwave or oven, adding a splash of milk if the sauce seems dry. This keeps the mac and cheese creamy and delicious.

Ingredient Substitutions

Feel free to replace whole wheat pasta with chickpea or lentil pasta for a gluten-free and protein boost. Use coconut milk instead of almond milk for a dairy-free option but expect a slightly different flavor. You can swap Dijon mustard with yellow mustard or omit it entirely if you prefer a milder sauce.

Serving Suggestions

Pair this baked mac and cheese with a simple green salad or steamed vegetables like asparagus or green beans for a balanced meal. For a heartier option, add cooked chicken or crispy bacon bits on top before baking.

Seasonal Adaptations

In spring and summer, add fresh peas or steamed spinach for vibrant color and freshness. During fall and winter, sprinkle in roasted butternut squash cubes or sweet potato for warmth and a touch of natural sweetness. These adjustments keep the dish feeling fresh and exciting year-round.

A close up of a baked mac and cheese dish.
A close up of a baked mac and cheese dish. | flavorrhaven.com

This dish brings a nutritious twist to a beloved comfort classic, making it a family favorite that's both wholesome and delicious.

FAQs about Recipes

→ What pasta works best for this dish?

Whole wheat elbow macaroni or any high-protein small pasta shapes hold the sauce well and provide a hearty texture.

→ Can I substitute the dairy ingredients?

Yes, low-fat milk can be replaced with unsweetened almond milk, and Greek yogurt adds creaminess without heavy fats.

→ How do I achieve a golden topping?

Mix whole wheat breadcrumbs with olive oil or melted butter and sprinkle over the pasta before baking for a crisp, golden crust.

→ Are there optional add-ins for extra nutrition?

Steamed cauliflower puree can blend into the sauce, and vegetables like broccoli, spinach, or peas can be added for variety and nutrients.

→ What baking temperature and time are recommended?

Bake uncovered at 375°F (190°C) for 20-25 minutes until the top is golden and bubbly.

Healthy Baked Mac Cheese

Whole wheat pasta with creamy cheese and yogurt sauce, baked until bubbly and golden.

Prep Time
15 mins
Cooking Time
25 mins
Overall Time
40 mins
Contributed by: Harper

Recipe Category: Comfort Food

Skill Level: Moderate

Cuisine Type: American

Recipe Output: 6 Portion Size

Dietary Features: Vegetarian-Friendly

What You'll Need

→ Pasta

01 8 oz whole wheat elbow macaroni or high-protein pasta

→ Sauce

02 1 ½ cups low-fat milk or unsweetened almond milk
03 1 tbsp all-purpose flour or whole wheat flour
04 ¾ cup plain Greek yogurt nonfat or low-fat
05 1 ½ cups shredded sharp cheddar cheese
06 ½ cup shredded part-skim mozzarella cheese
07 1 tsp Dijon mustard
08 ½ tsp garlic powder
09 ½ tsp onion powder
10 ¼ tsp salt, adjust to taste
11 ¼ tsp black pepper
12 Optional: 1 cup steamed cauliflower puree

→ Topping

13 ⅓ cup whole wheat breadcrumbs or crushed almonds
14 1 tbsp olive oil or melted butter

→ Optional add-ins

15 Steamed broccoli, spinach, peas, or cooked chicken

Step-by-Step Guide

Step 01

Preheat oven to 375°F. Lightly grease a 9×9-inch baking dish or similar casserole dish.

Step 02

Cook the pasta according to package instructions until al dente. Drain and set aside.

Step 03

In a medium saucepan over medium heat, whisk flour and milk together until smooth and slightly thickened, about 3–4 minutes.

Step 04

Reduce heat to low. Stir in Greek yogurt, shredded cheeses, Dijon mustard, garlic powder, onion powder, salt, and black pepper. Mix until cheese melts and sauce is smooth. If using, stir in steamed cauliflower puree.

Step 05

Pour sauce over cooked pasta and mix thoroughly to coat evenly.

Step 06

Spoon mixture into prepared baking dish and spread evenly.

Step 07

Mix breadcrumbs with olive oil or melted butter and sprinkle evenly over pasta.

Step 08

Bake uncovered for 20–25 minutes until topping is golden and bubbly.

Step 09

Allow dish to cool slightly for optimal texture and flavor before serving.

Additional Notes

  1. Adjust salt to taste and consider adding optional steamed vegetables or chicken for added nutrition.

Tools You'll Need

  • 9×9-inch baking dish
  • Medium saucepan
  • Whisk
  • Colander

Allergen Notices

Inspect every ingredient for potential allergens and seek expert advice if necessary.
  • Contains dairy and gluten; may contain nuts if almonds are used in topping.

Per Serving Nutritional Info

Keep in mind these are general guidelines, not a replacement for professional advice.
  • Calories: 360
  • Fats: 9 grams
  • Carbohydrates: 42 grams
  • Proteins: 22 grams