Boil the pasta: Bring a large pot of salted water to a boil.
Cook the pasta until just shy of al dente. Reserve 1/2 cup of the pasta water, then drain.
Prep the skillet: While the pasta cooks, heat 1 tablespoon olive oil in a large skillet over medium-high heat.
Cook the chicken: Season chicken with salt and pepper. Add to the hot skillet and cook, stirring occasionally, until golden and cooked through, 5–7 minutes.
Transfer to a plate.
Sauté asparagus: Add the remaining tablespoon of olive oil to the skillet. Add asparagus and a pinch of salt. Cook 3–5 minutes, stirring, until crisp-tender and bright green.
Add aromatics: Push asparagus to the side.
Add garlic and red pepper flakes to the center. Cook 30 seconds until fragrant, then toss with the asparagus.
Combine: Return chicken to the skillet. Add drained pasta, pesto, lemon zest, and 2–3 tablespoons pasta water.
Toss over low heat until glossy and well coated, 1–2 minutes.
Finish: Stir in Parmesan and a squeeze of lemon juice. Add more pasta water if needed to loosen the sauce. Taste and adjust salt, pepper, and lemon.
Serve: Top with extra Parmesan and a pinch of red pepper flakes if you like.