Bring 4-6 quarts of water lightly salted with 1 teaspoon salt to a boil. Add elbow pasta and boil for 5-7 minutes until al dente, or as directed by package instructions. Drain and rinse with cold water to prevent overcooking, then set aside.
Using an immersion blender or food processor, blend cottage cheese until a smooth, creamy consistency is achieved.
Preheat oven to 350°F. In a large mixing bowl, gently fold cottage cheese, sour cream, 1 beaten egg, mustard, nutritional yeast, and seasonings into the macaroni noodles. Then shred cheddar cheese and smoked gouda, and gently fold in.
Lightly grease a large baking dish, then transfer mac and cheese, spreading in an even layer. Top with additional shredded cheddar, gouda, and parmesan cheese and bake for 20-25 minutes. Dust with a pinch of smoked paprika, black pepper, and freshly chopped chives.
Notes
Protein pasta tends to absorb more liquid than traditional pasta. To keep the mac creamy, try to avoid overbaking. You can mix in a splash of milk or reserved pasta water if needed.
You may want to boil the pasta 2 minutes shy of al dente since we'll also be baking it. This will help prevent mushy mac and cheese.
I recommend using blocks of cheese and shredding them yourself rather than buying pre-shredded cheese. Freshly shredded cheese melts better and will result in a creamier texture.
If you prefer a breadcrumb-like topping on your mac & cheese, you can use crushed pork rinds as a high-protein alternative.
Optionally, you can broil the mac & cheese for 1-2 minutes after baking to lightly brown the cheese topping.
Store leftover high protein macaroni and cheese in an airtight container in the refrigerator for up to 4 days.
To reheat, you can microwave individual portions for 30 seconds at a time until heated through. You can mix in a splash of milk or water to restore creaminess.