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 olive oil in a large nonstick skillet over medium heat. Add the chicken breast pieces and cook for 5-7 minutes, stirring occasionally, until cooked through and no longer pink inside. Remove from heat and set aside.
In a medium saucepan, whisk together the all-purpose flour and skim milk over medium heat. Continue whisking until the mixture thickens and begins to bubble, about 5 minutes.
Reduce heat to low and stir in the reduced-fat shredded cheddar cheese and mozzarella cheese until melted and smooth.
Add garlic powder, onion powder, ground black pepper, and salt to the cheese sauce and stir to combine.
Remove the cheese sauce from heat and stir in the plain nonfat Greek yogurt until fully incorporated.
Add the cooked chicken and drained macaroni to the cheese sauce. Stir gently until everything is evenly coated with the sauce.
Serve immediately while warm.