High Protein Baked Mac and Cheese

03/14/2026
ByKatelyn Anne

There’s nothing quite like baked mac and cheese that’s creamy on the inside, golden and bubbly on top, and packs over 40 grams of protein into every serving. It’s easy enough to throw together on a weeknight and good enough to meal prep on repeat every single week.

Why You'll Love This Recipe

I started making this when I wanted the full comfort of baked mac and cheese but needed it to actually fit my nutrition goals. The cottage cheese and Greek yogurt together are what push each serving past 40 grams of protein without you having to add anything extra to the dish. Blending them completely smooth is what makes the sauce taste rich and creamy.

Ingredients

Pasta

1 lb (450g) elbow macaroni or chickpea pasta
salt, for the pasta water

Cheese Sauce

1 cup cottage cheese
3/4 cup plain Greek yogurt
1/2 cup whole milk, warmed
1 tbsp cornstarch
1 tbsp minced garlic (about 3 cloves)
2 tsp smoked paprika
1 1/2 tsp dry mustard powder
1/2 tsp black pepper
1/2 tsp salt
pinch of nutmeg
pinch of cayenne
1 1/2 cups sharp cheddar, freshly grated
1/2 cup Parmesan, freshly grated

Topping

1 1/2 cups shredded Colby jack or mozzarella
1/4 cup panko breadcrumbs
olive oil spray

Instructions

1. Cook the Pasta

Bring a large pot of well salted water to a rolling boil and cook the pasta one to two minutes under the package’s recommended time so it’s just shy of al dente. It’ll keep cooking in the oven and you want it to stay firm rather than turning soft and mushy once baked. Drain it thoroughly but don’t rinse it. The starch left on the surface of the pasta helps the sauce cling to every single piece.

2. Make the Sauce Base

Add the cottage cheese, Greek yogurt, warmed milk, cornstarch, garlic, smoked paprika, mustard powder, black pepper, salt, nutmeg, and cayenne to a blender and blend until completely smooth with no lumps remaining. This step is what transforms everything into a silky, creamy base. Pour the blended mixture into a medium saucepan over medium heat and stir continuously for 3 to 5 minutes until it thickens noticeably.

3. Add the Cheese

Reduce the heat to low and stir in the grated sharp cheddar and Parmesan a handful at a time, stirring well between each addition. Adding it gradually rather than all at once prevents the cheese from clumping or seizing and gives you a completely smooth, velvety sauce. Always grate your own cheese here because pre-shredded cheese is coated in anti-caking agents that stop it from melting properly. Once the sauce is fully smooth, taste and adjust the salt and pepper.

4. Combine and Assemble

Preheat your oven to 400°F (200°C) and lightly grease an 8×8 inch baking dish. Add the drained pasta straight into the saucepan with the cheese sauce and stir until every piece is fully coated. Pour everything into the prepared baking dish and smooth it out evenly. Scatter the shredded Colby jack or mozzarella over the top, then sprinkle the panko breadcrumbs evenly and give everything a light spray of olive oil so the crumbs brown in the oven.

5. Bake and Broil

Bake uncovered at 400°F (200°C) for 15 to 20 minutes until the cheese on top is melted and bubbling. Then switch the oven to broil for 2 to 3 minutes until the top turns golden and crisp, watching it closely the entire time because it can go from perfectly golden to burnt very fast. Pull it out and let it rest for 5 minutes before serving. That short rest lets the sauce tighten up so it scoops cleanly rather than running across the plate.

Tips

Always grate your own cheese. Pre-shredded cheese contains cellulose and starch coatings that prevent it from melting smoothly into a sauce. Freshly grated cheese melts into the base evenly and gives you that glossy, velvety finish that makes baked mac and cheese worth making from scratch.
Blend the cottage cheese completely smooth. Two minutes in the blender transforms it into a seamless, creamy base that melts right into the sauce and tastes indistinguishable from a full fat cream sauce.
Warm your milk before adding it. Cold dairy added to a warm sauce base causes the temperature to drop suddenly, which makes the sauce seize and turn lumpy. Warming it first keeps everything at a consistent temperature and helps the sauce come together smoothly.
Pull the pasta out early. Cooking it one to two minutes under al dente before baking is the difference between pasta that holds its shape and stays slightly firm in the sauce, and pasta that turns soft and loses its texture entirely once it spends time in the oven.
Let it rest before serving. Five minutes out of the oven allows the sauce to set so the mac and cheese scoops cleanly and holds together on the plate.

Variations and Substitutes

For extra protein, stir shredded rotisserie chicken through the pasta before it goes into the baking dish. It adds lean protein without changing the flavor of the dish at all, and the chicken stays moist baked into the sauce. It also makes the whole thing a complete meal rather than a side dish.
To make this gluten free, swap the elbow macaroni for your favorite gluten free pasta and replace the panko breadcrumbs with crushed gluten free crackers or simply leave the topping off. The sauce itself is already gluten free so the swap is straightforward and the texture holds up well after baking.
For a more indulgent version closer to a classic baked mac and cheese, swap the cottage cheese and Greek yogurt for 2 cups of warm heavy cream and add 2 tablespoons of softened cream cheese to the sauce. Build the rest of the recipe the same way. The sauce is richer and the flavor is deeper, which makes it a great option for holidays or when you want the full comfort food version.

Storage and Reheating

Refrigerating

Store leftovers in an airtight container in the fridge for up to 4 days.

Freezing

Let the mac and cheese cool completely, then transfer to a freezer-safe airtight container and freeze for up to 2 months. Thaw overnight in the fridge before reheating.

Reheating

Microwave: Place a portion in a microwave-safe bowl, add a small splash of milk, cover loosely, and heat in 60-second intervals on medium power, stirring between each, until heated through and creamy again.
Oven: Transfer to an oven-safe dish, add a splash of milk, cover with foil, and warm at 350°F (175°C) for 15 to 20 minutes until heated through and bubbling at the edges.

High Protein Baked Mac and Cheese

Protein-packed baked mac and cheese with a golden broiled top and over 40 grams of protein per serving in every bite. The sauce is built from blended cottage cheese and Greek yogurt which makes it rich and velvety without the heaviness of a full cream base. It's meal prep friendly, endlessly satisfying, and tastes nothing like a healthy swap.

Print Recipe Pin Recipe

Prep Time 15

Cook Time 25

Total Time 40

Course Main Course

Servings 4

Ingredients

1 lb 450g elbow macaroni or chickpea pasta
1 cup cottage cheese
3/4 cup plain Greek yogurt
1/2 cup whole milk warmed
1 tbsp cornstarch
1 tbsp minced garlic
2 tsp smoked paprika
1 1/2 tsp dry mustard powder
1/2 tsp black pepper
1/2 tsp salt
pinch of nutmeg
pinch of cayenne
1 1/2 cups sharp cheddar freshly grated
1/2 cup Parmesan freshly grated
1 1/2 cups shredded Colby jack or mozzarella
1/4 cup panko breadcrumbs
olive oil spray

Instructions

Bring a large pot of salted water to a boil and cook the pasta one to two minutes under the package time. Drain but don't rinse.
Blend the cottage cheese, Greek yogurt, warmed milk, cornstarch, garlic, smoked paprika, mustard powder, black pepper, salt, nutmeg, and cayenne until completely smooth.
Pour the blended mixture into a saucepan over medium heat and stir continuously for 3 to 5 minutes until thickened. Reduce to low and stir in the cheddar and Parmesan a handful at a time until the sauce is completely smooth.
Preheat the oven to 400°F (200°C) and grease an 8x8 inch baking dish. Stir the drained pasta into the sauce until fully coated, then pour into the baking dish and smooth out evenly.
Top with the shredded Colby jack or mozzarella, scatter the panko breadcrumbs evenly over the top, and spray lightly with olive oil.
Bake uncovered for 15 to 20 minutes until bubbling, then broil for 2 to 3 minutes until the top is golden and crisp. Rest for 5 minutes before serving.

Notes

Always grate your own cheese. Pre-shredded cheese contains anti-caking coatings that prevent it from melting smoothly, and freshly grated cheese is what gives the sauce that glossy, velvety finish.
Blend the cottage cheese completely smooth before adding it to the pan. Two minutes in the blender transforms it into a seamless base that melts right into the sauce and tastes indistinguishable from a full fat cream sauce.
Cook the pasta one to two minutes under al dente. It finishes cooking in the oven and pulling it early is what keeps it firm and perfectly coated in the finished dish.
For extra protein, stir shredded rotisserie chicken through the pasta before baking. It adds lean protein without changing the flavor and turns the whole thing into a complete meal.