Two men, aged 56 and 53, and one women, 52, fleeing from the storm died while sheltering in a garden shed in Düsseldorf, when a poplar tree collapsed on the building on Monday evening.
Emergency services were able to rescue six others from building, two of whom were severely injured.
A 50-year old cyclist in Cologne and a second cyclist in Krefeld, North Rhine-Westphalia, also died when they were hit by falling trees. A sixth person, a 49-year-old man, collapsed and died as he was clearing up storm damage in Essen.
Heavy rain, lighting and hail also caused traffic delays on the railway, motorway and airports. Düsseldorf airport closed for an hour on Monday evening due to winds of up to 150 km/h.
Rail operator Deutsche Bahn reported severe delays as fallen debris obstructed railway lines. Although several lines were cleared on Monday evening, many connections remained blocked on Tuesday morning, including lines around Dortmund, Essen, Düsseldorf, Gelsenkirchen, Duisburg and Cologne. Emergency bus transportation was not possible in some ares due to storm damage.
The storm headed northeast early Tuesday morning and lessened in magnitude.
New storm fronts are currently moving towards the Rhine, Ruhr and Black Forest areas, a spokesperson for the German Weather Service (DWD) said on Tuesday morning. Whether those storms will be as strong as those in North Rhine-Westphalia remains unclear.
More showery and thundery weather is forecast fro the north and west on Wednesday night.
The storm front closes in near Düsseldorf on Monday night.