Cook the pasta: Bring a large pot of salted water to a boil. Add pasta and cook until al dente according to package directions. Reserve 1/2 cup pasta water, drain, and set aside.
Mix the fajita seasoning: In a small bowl, combine 2 teaspoons chili powder, 1 teaspoon smoked paprika, 1 teaspoon cumin, 1/2 teaspoon oregano, 1/2 teaspoon garlic powder, 1/2 teaspoon onion powder, 1/2 teaspoon salt, and 1/4 teaspoon black pepper.
Prep the chicken: Slice chicken into thin strips.
Pat dry and toss with half the seasoning and 1 teaspoon oil.
Sear the chicken: Heat a large skillet over medium-high. Add 1 tablespoon oil. Cook chicken in a single layer, 3–4 minutes per side, until browned and cooked through.
Transfer to a plate and keep warm.
Sauté the veggies: In the same skillet, add another teaspoon oil if needed. Add sliced onion and bell peppers with a pinch of salt. Cook 5–7 minutes, stirring occasionally, until tender with light char.
Add minced garlic and the remaining seasoning; cook 30 seconds until fragrant.
Build the sauce: Pour in chicken broth and bring to a simmer, scraping up any browned bits. Stir in the cooked chicken (and fire-roasted tomatoes if using). Lower heat to medium-low.
Make it creamy: In a small bowl, whisk Greek yogurt with a few tablespoons of warm broth from the pan to temper it.
Stir the tempered yogurt into the skillet. Keep heat low to prevent curdling. Add a splash of reserved pasta water if you want a looser sauce.
Add the pasta: Toss in the cooked pasta and fold to coat.
Squeeze in the juice of 1 lime and add lime zest. Taste and adjust salt, pepper, and heat. If using, sprinkle in the cheese and let it melt.
Finish and serve: Top with chopped cilantro, green onions, and sliced jalapeño if you like it spicy.
Serve hot with extra lime wedges.