Cook the elbow macaroni according to package instructions until al dente. Drain and set aside.
In a large skillet, heat olive oil over medium-high heat. Add the sliced chicken breast and season with chili powder, cumin, smoked paprika, cayenne pepper, salt, and black pepper. Cook for 5-7 minutes, stirring occasionally, until the chicken is cooked through and lightly browned. Remove chicken from skillet and set aside.
In the same skillet, add the sliced onions and bell peppers. Cook for 5-6 minutes until the vegetables are softened and slightly caramelized. Add the minced garlic and cook for an additional 1 minute. Remove from heat and set aside.
In a medium saucepan, melt the butter over medium heat. Whisk in the flour and cook for 1-2 minutes, stirring constantly, to form a roux.
Gradually whisk in the milk, continuing to whisk until the mixture thickens and begins to bubble, about 4-5 minutes.
Remove the saucepan from heat and stir in the shredded cheddar and mozzarella cheeses until melted and smooth.
Stir in the Greek yogurt until fully combined and creamy.
Add the cooked macaroni, chicken, and sautéed vegetables to the cheese sauce. Stir gently to combine all ingredients evenly.
Sprinkle chopped fresh cilantro over the top and mix lightly.
Serve the high protein chicken fajita mac n cheese warm.