The storms hit during the afternoon, triggering flash floods that swept away a man who was forced to abandon his car. Police said that the man managed to make it to high ground.
Another man was killed when he was struck by lightning whilst working in a field as the fierce storms raged overhead.
Substantial damage was caused across the island, with cars overturned, trees uprooted and homes flooded.
Malta’s meteorological service said that 42.4mm of rain fell in just two hours, which is more than the 40mm that would be expected for the whole of September.
Further showers and thunderstorms are possible in the next few days but they aren’t expected to be as severe.