The two detached houses, which were close to each other, were hit between 8pm and 9pm, causing damage to their chimneys, interior walls and electrical wiring, Fribourg police said in a statement.
Thankfully no one was hurt, and the occupants were allowed to return home after the houses had been checked by emergency workers and an electrician.
Around a dozen other houses were flooded in the Fribourg area, said police.
The storm also hit the canton of Vaud – where French president Emmanuel Macron was visiting Lausanne – and parts of German-speaking Switzerland, with heavy rain and strong winds in the cantons of Bern, St Gallen and Lucerne.
Monday's storm came two days after another severe storm caused millions of francs worth of damage in Zofingen in the canton of Aargau on Saturday night.