A 26-year-old man was driving an all-terrain vehicle near Hauzenberg in Passau county when a tree fell on him and he later died of his injuries, police reported.
Several other people in the region were injured in weather-related accidents too. In Waldenreut a man fell from his roof after attempting to repair storm damage and suffered a shoulder injury.
Meanwhile a woman near Waldkirchen was hospitalised after being struck by lightning in her car.
A family of four camping near Ottach in lower Bayern narrowly escaped with their lives when heavy gusts pushed their camper wagon 30 metres into the Danube river.
Police closed the A8 motorway between Adelzhausen and Odelzhausen due to heavy rainfall and gale force winds overnight.
Uprooted trees caused most of the 140 accidents police reported overnight. Many residents also reported flooded cellars.
The tempest also hit the world's largest hops-growing area of Hallertau. Farmers feared more than 2,500 hectares of the total 15,000 hectares planted were damaged by heavy rain.
In the nearby state of Baden-Württemberg, a train derailed after hitting several uprooted trees on the tracks. The conductor was badly injured when a tree bored into the driving compartment, and 75 passengers were evacuated, police reported.
A farm near Amtzell caught fire due to lightning, burning 10 cows in a barn to death and causing some €200,000 in damages.
In Konstanz near the Bodensee police reported that the city was covered with at least 10 centimetres of hail for a time. Wind gusts as high as 113 kilometres per hour were also recorded. Train traffic to the city had to be blocked to clean up felled trees and damaged power lines. Authorities estimated several million euros in hail and wind damage to roofs, windows and vehicles.
“It looks like a bomb went off here,” a police spokesperson said.
Authorities also closed roads in Esslingen due to falling trees and the several flights from the Stuttgart airport were delayed after the runway closed due to lightning in the early evening.
In the north, on the Weser River near Bremerhaven, police reported that strong winds pushed a Norwegian freighter into three other boats while it was in the docks. In a separate incident a Lebanese ship sustained damage and lost a container overboard.
In Braunschweig, police received more than 100 calls for emergency assistance when trees were uprooted, blocking roads and doors to people's homes. A spokesperson for the fire department said no one there was injured.
As the nasty weather moved south, parts of Austria were also walloped with thunder storms, heavy rain and strong winds throughout Tuesday night. More than 2,700 lightning strikes were recorded in the states of Salzburg and Upper Austria. In Switzerland, a tree landed on a 31-year-old man while he was driving.