Two of the flights, arriving from Thessaloniki, Malta, lacked sufficient fuel to circle Manchester and await improved weather conditions, while the third, from Corfu, was also diverted.
After refuelling in Newcastle, the aircraft returned to Manchester once the storms cleared, with one flight landing over three hours behind schedule.
A Royal Jordanian flight, also low on fuel, was granted a priority landing at Manchester rather than being diverted.
Manchester Airport stated that the overall disruption caused by the thunderstorms was minimal, with normal operations quickly restored.