Bring a large pot of salted water to a boil and cook the linguini until al dente. I always reserve a little pasta water just in case I need to loosen the sauce later. Drain and set aside while preparing the rest.
Heat olive oil in a large skillet over medium-high heat. Add garlic, shallot, and both types of mushrooms. Cook until soft and fragrant, stirring occasionally to prevent burning.
Add the chicken pieces to the skillet and season with salt, pepper, and red pepper flakes. Cook until the chicken is golden on the outside and fully cooked inside. Stir gently so the chicken stays juicy.
Add the cooked pasta to the skillet along with lemon zest, lemon juice, and chives. Toss everything together until well combined. Sprinkle in the cheese and stir until melted and creamy.