Hundreds of emergency calls were made to police and firefighters by people needing help to deal with damage from the strong winds, heavy rainfall, and hailstones.
The states of Salzburg and Upper Austria were particularly affected, with thousands of firemen deployed to help clear flooded cellars and repair roofs that had blown off in the wind.
In the town of Annaberg the highway B162 was blocked for 500 metres by a mudslide and the A8 in the direction of Wels was also blocked by fallen trees.
The town of Imst in Tyrol was also heavily affected with firemen working through the night to clear the town centre of flood water.
Some regions - as far away as Innsbruck and Vienna - saw a hot and muggy Monday morning followed by sudden hailstorms.
Rain showers and thunderstorms are predicted to continue in some areas on Tuesday, with the national weather service ZAMG issuing a country-wide storm warning.
Particularly heavy rain is expected from Vorarlberg to Upper Austria, which will also be hit by a cold front coming over the Alps from Scandinavia.
The thermometer gauge will range from 17 to 35 degrees Celsius in the country, with the east and south of Austria seeing warmer temperatures although rainstorms are also expected there.