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.
In a medium saucepan, melt the unsalted butter over medium heat.
Whisk in the all-purpose flour and cook for 1-2 minutes, stirring constantly, to form a roux.
Gradually whisk in the low-fat milk, continuing to whisk until the mixture is smooth and begins to thicken, about 5 minutes.
Reduce the heat to low and stir in the shredded reduced-fat sharp cheddar cheese and low-fat mozzarella cheese until fully melted and smooth.
Add the garlic powder, onion powder, smoked paprika, black pepper, and salt to the cheese sauce. Stir to combine.
Add the cooked and shredded chicken breast to the cheese sauce and stir well to incorporate.
Add the drained macaroni to the saucepan and gently fold to combine all ingredients evenly.
Transfer the mac and cheese to a serving dish and sprinkle the grated Parmesan cheese on top.
Serve immediately while warm.