The northern states of Lower Saxony and Saxony-Anhalt were hit with the most severe weather, bringing floods and property damage.
Schools in the Leer district of Lower Saxony closed for the day out of concern that students would be hurt by falling trees. Deutsche Bahn reported massive delays due to felled trees on tracks in the area. Meanwhile two drivers lost control of their vehicles on wet roads and collided with trees.
The A31 motorway and an Ems River tunnel were closed briefly due to flooding, police said.
While rain fell at a rate of 25 to 40 litres per square metre in an hour in northern Saxony-Anhalt, the German Weather Service (DWD) cancelled severe weather warnings for western states, calling for thunder storms instead.
Monthly rainfall for this time of year in the region usually averages some 50 litres per square metre, a DWD spokesperson said.
The central state of Hesse also suffered from severe storms. A lightning strike struck a family home in Viernheim setting the roof on fire. Police said the parents were able to escape the home with their 11 and 14-year-old children unharmed.
Police also closed the Lohberg tunnel in southern Hesse after a lightning strike shut down technical operations.
In many places storms arrived after an eerily hot and still morning. The DWD reported the nasty weather was due to subtropical air clashing with a cold front moving from west to east over the country.