Many of the roughly 600 emergency calls involved flooded basements and blocked roads due to fallen trees and stray branches.
No-one has been injured, but the weather caused widespread power outages and damage in the state, which was just recovering from a previous storm on July 11 that caused torrential rains and landslides.
In the Deggendorf district several power poles were bent by the storm, leaving surrounding communities without electricity. A few kilometres away, a wind gust tore a hole in the top of an indoor arena. One family lost their entire roof in the storm.
On the A92 motorway, a strong gust of wind threw a truck across one lane of traffic, causing delays for several hours.
Trains were affected too, causing temporary blockages – some of which had not been cleared by Thursday morning.
Weather in much of southern Germany looked set to stay stormy on Thursday, with rain and wind throughout much of the region.