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 8-10 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large nonstick skillet over medium heat. Add the chicken pieces and cook until fully cooked through and no longer pink in the center, about 6-8 minutes. Remove from heat and set aside.
In a medium saucepan, whisk together the all-purpose flour and skim milk over medium heat. Continue whisking constantly until the mixture thickens and starts to bubble, about 5-7 minutes.
Remove the saucepan from heat and stir in the shredded reduced-fat sharp cheddar cheese and shredded reduced-fat mozzarella cheese until melted and smooth.
Add garlic powder, onion powder, ground black pepper, and salt to the cheese sauce and stir to combine.
Stir in the plain nonfat Greek yogurt to add creaminess and tanginess to the sauce.
Add the cooked macaroni and chicken pieces to the cheese sauce and stir gently until everything is well coated.
Return the skillet to low heat and cook for an additional 2-3 minutes, stirring occasionally, until heated through.
Serve immediately.