Preheat and prep the pan. Heat your oven to 375°F (190°C). Lightly spray a 12-cup muffin tin with nonstick spray.
Warm and shape the tortillas. Briefly microwave the tortillas for 20–30 seconds to make them flexible.
Press each tortilla gently into the muffin cups, pleating the edges as needed so they form a little bowl.
Par-bake for structure. Bake the tortilla cups for 6–8 minutes until they start to firm up but aren’t fully crisp. Remove and set aside.
Season the chicken. Slice the chicken into small, bite-size strips. Toss with 1 tablespoon oil, fajita seasoning, a squeeze of lime, and a pinch of salt and pepper.
Cook the chicken. Heat a large skillet over medium-high.
Add the chicken and cook 5–7 minutes, stirring occasionally, until cooked through and lightly browned. Transfer to a bowl and cover.
Sauté peppers and onions. In the same pan, add a touch more oil if needed. Cook the sliced peppers and onions with a pinch of salt for 5–6 minutes until tender-crisp with a bit of char.
Squeeze in more lime to brighten.
Make the creamy high-protein topping. In a small bowl, stir together Greek yogurt (or blended cottage cheese) with a pinch of salt, pepper, and a squeeze of lime. If you like heat, add a few drops of hot sauce.
Assemble the cups. Divide the chicken among the tortilla cups. Top with sautéed peppers and onions.
If using cheese, add a light sprinkle to each cup.
Bake to finish. Return the tray to the oven for 5–7 minutes, just until the tortillas are crisp and the cheese (if using) melts.
Garnish and serve. Let the cups cool for 2–3 minutes. Add a small spoonful of the creamy topping, sprinkle with cilantro, and serve with lime wedges.