Heavy rain and high winds associated with thunderstorms can also cause issues during the different stages of the flight, especially during takeoff and landing. Wind shear, a sudden change in wind speed and direction, can create challenging conditions for pilots trying to land the airplane safely.

Modern commercial aviation is designed with the philosophy of avoidance rather than confrontation when it comes to thunderstorms. While it is technically possible for an aircraft to land during storm conditions, pilots and air traffic controllers take safety extremely seriously and will rarely attempt a landing if a severe storm is directly over the airfield. Thunderstorms present several major hazards, most notably wind shear and microbursts, which are sudden, violent changes in wind speed and direction that can rob an aircraft of lift during the critical landing phase. Modern planes are equipped with advanced onboard weather radar and Predictive Windshear Systems to alert pilots of these dangers. If a storm is deemed too risky, the aircraft will enter a "holding pattern" to wait for the weather to clear or divert to a pre-planned alternate airport. Lightning strikes, while visually dramatic, are generally not a major threat to the plane's structural integrity because the metal fuselage acts as a Faraday cage, safely conducting the electricity around the exterior of the cabin.