The eerie green clouds which preceded today's storm were a sign of things to come, according to Times of Malta reader and weather enthusiast Andrea Muscat.
Mr Muscat said that the Mesoscale Convective System which formed to the south-west of the Maltese Islands on Tuesday evening approached the Maltese islands slowly overnight.
A number of heavy rain showers preceded the storm, which made landfall just before sunrise.
"It is nature's own means of warning us of the imminent. The high water content of more intense thunderstorms absorbs red light from incoming sunlight, resulting in a distinct green coloration.
Watch: Thunderstorm disrupts flights, damages road in Mellieħa
"More specifically, thunderstorms with blue-green clouds indicate larger rain drops, while yellow-green clouds indicated smaller rain drops."
Lightning detectors recorded around 100,000 lightning strikes around the Maltese Islands.
At its most active, the thunderstorm was producing up to 175 strikes per minute. The majority were cloud-to-cloud and posed little danger. The few cloud-to-ground strikes, however, proved to be a great threat, because most struck land.
Gozo was by far the hardest. The wettest locality was Għarb with a staggering 84.2mm of rain, or a whole October's worth of rainfall. No locality in Gozo received less than 50mm of rain.
The wettest in Malta was Birżebbuġa with a total of 52.8mm of rain. Most localities in Malta received between 20mm and 40mm of rain.
The 'driest' was the north-west of Malta with around 15mm of rain.
More bad weather is likely to occur tomorrow, before improving substantially on Friday.