Bring a large pot of salted water to a boil. Add the whole wheat elbow macaroni and cook according to package instructions until al dente, about 8-9 minutes. Drain and set aside.
While the pasta cooks, heat the olive oil in a large skillet over medium-high heat. Add the finely chopped onion and cook for 3-4 minutes until softened.
Add the minced garlic to the skillet and cook for an additional 30 seconds until fragrant.
Add the lean ground beef to the skillet. Cook, breaking it up with a spoon, until browned and cooked through, about 6-7 minutes. Drain any excess fat and set the beef mixture aside.
In a medium saucepan, melt the unsalted butter over medium heat. Once melted, whisk in the all-purpose flour and cook for 1-2 minutes until the mixture is lightly golden and bubbling.
Gradually whisk in the low-fat milk, continuing to whisk constantly to avoid lumps. Cook the sauce, stirring frequently, until it thickens, about 5 minutes.
Remove the sauce from heat and stir in the shredded sharp cheddar cheese and shredded mozzarella cheese until fully melted and smooth.
Season the cheese sauce with salt, ground black pepper, and smoked paprika. Stir well to combine.
Add the cooked macaroni and the ground beef mixture to the cheese sauce. Stir gently until all ingredients are evenly combined and heated through.
Serve the high protein ground beef mac n cheese hot, garnished if desired.