Bring a large pot of salted water to a boil. Add the elbow macaroni and cook according to package instructions until al dente, about 7-8 minutes. Drain and set aside.
In a small bowl, combine chili powder, ground cumin, smoked paprika, garlic powder, onion powder, cayenne pepper, 1/4 teaspoon salt, and 1/8 teaspoon black pepper. Mix well to create fajita seasoning.
Heat olive oil in a large skillet over medium-high heat. Add the sliced chicken breast and sprinkle half of the fajita seasoning over the chicken. Cook, stirring occasionally, until the chicken is cooked through and lightly browned, about 5-7 minutes. Remove chicken from the skillet and set aside.
In the same skillet, add the sliced red bell pepper, green bell pepper, and yellow onion. Sprinkle the remaining fajita seasoning, 1/4 teaspoon salt, and 1/8 teaspoon black pepper over the vegetables. Sauté until the vegetables are tender-crisp, about 5 minutes. Remove from heat.
In a medium saucepan, melt the butter over medium heat. Once melted, whisk in the flour and cook for 1-2 minutes, whisking constantly, to form a roux.
Gradually whisk in the milk, continuing to whisk until the mixture is smooth. Cook, stirring frequently, until the sauce thickens and coats the back of a spoon, about 5-7 minutes.
Remove the sauce from heat and stir in the shredded cheddar cheese and Monterey Jack cheese until melted and smooth.
Stir in the Greek yogurt until fully incorporated.
Add the cooked macaroni, sautéed chicken, and vegetables to the cheese sauce. Gently fold everything together until well combined and heated through.
Serve the high protein chicken fajita mac n cheese garnished with chopped fresh cilantro and lime wedges on the side.