The high-speed ICE rail line between Berlin and Düsseldorf was completely cancelled on the section between Bielefeld and Gütersloh on Friday morning. The long-distance service had instead been redirected through Osnabrück.
High-speed services between Hanover and Hamburg was also still not running, having been cancelled on Thursday afternoon. Services are expected to resume on Friday afternoon, but on a redirected route - meaning frustrating delays for people travelling home for the weekend.
There was some good news though, as regular services between Hamburg and Bremen had resumed on Friday.
On Thursday and early Friday morning gale-force winds, torrential rains and hail damaged rail tracks and power lines, forcing trains to be halted between Berlin, Hamburg, Bremen, Kiel and Hanover.
Video footage was recorded of lightning striking Berlin's Fernsehturm, the tallest building in Germany.
A 50-year-old man died while his wife was injured when their parked car was hit by a falling tree near the city of Uelzen. A falling tree also seriously injured a female cyclist nearby.
An 83-year-old woman meanwhile died in Gifhorn in the neighbouring state of Lower Saxony after her car hit a tree which had been blown across the street in strong gales, police said.
In the port city of Hamburg, the weather service reported a rare tornado some 10 kilometres from the airport.
In the south of the city, storms damaged house roofs and killed sheep that were hit by toppled trees.
Music fans had to seek shelter in their cars at the venue of a weekend musical festival near Bremen that, ironically, is named "Hurricane".