People were warned to stay home as trees were felled and roofs torn off during the gale-force winds, whipped up when a plume of hot air from Africa collided with cooler air from northern Europe.
German authorities said 10 of those hurt were seriously injured. Pictures posted to social media showed an apparent tornado with its distinctive spinning cyclone flinging debris through the air, though the German Weather Service did not immediately confirm a tornado had occurred.
A 38-year-old man in the far-western town of Wittgert died of head injuries sustained when he fell after suffering an electric shock in a flooded cellar, local media quoted police as saying.
Police said up to 40 people had been injured in Paderborn, a town of some 150,000 halfway between Frankfurt and Hamburg. Rail and road transport were disrupted throughout the region.
In nearby Hellinghausen, images shared on social media showed that a steeple had been ripped from the roof of a church tower, its remains scattered around the churchyard.
Police posted images showing trees felled or split in half, as well as roofs that had been swept clean of tiles by the winds in Paderborn.
“Some 40 people were injured in the storm, at least 10 of them seriously,” city police said in a statement. “Sheeting and insulation were blown kilometres (miles) away. Countless roofs are uncovered or damaged. Many trees still lie on destroyed cars.”
They asked locals to stay at home. The German Weather Service warned that the stormy weather was set to continue.
Residents of Lippstadt, a town about 22 miles west Paderborn, were hit with heavy rain and hail as the weather system wreaked havoc in towns across the west of the country. A church steeple in the town was toppled.
In Cologne, schools closed before midday to give students time to make it home safely before the storm hit. Meteorologists said the stormy weather is likely to continue in the coming days.
The weather in Germany is in stark contrast to the conditions in Spain, which is experiencing an extreme heatwave. The warm weather is being caused by a mass of hot, dry air carrying dust coming from northern Africa.
It has pushed temperatures some 15C above average, with the mercury topping 40C (104F) in some regions . The State Meteorological Agency said it expected the “unusual and extreme” temperatures to peak on Saturday. “These will probably be among the warmest temperatures we’ve seen in May in the 21st century,” agency spokesman Ruben del Campo said.