The persecution of the Jews started in September and October, 1348, at Chillon, on the Lake of Geneva, where the first criminal proceedings were instituted against them, after they had long before been accused by the people of poisoning the wells. Similar scenes followed in Bern and in Freiburg, in 1349.

The tortured Jews confessed themselves guilty of the crime imputed to them. In the autumn of 1348 a dreadful panic, caused by this supposed poisoning, seized all nations; in Germany, especially, the springs and wells were built over and for a long time the inhabitants of numerous towns and villages used only river and rainwater. The city gates were also guarded with the greatest caution: only confidential persons were admitted.

The Flagellants had helped to spread the belief that Jews infected cities' wells with the Plague element through the use of contaminated bottles. Fears were increased when it was discovered that Jews did not take water from city wells. In September, 1348, eleven Jews were charged with contaminating a well in a small southern German town. The men were tortured, and each confessed (falsely) to the crime. Their trial and executions set a wave of terrible acts against Jews in Switzerland and Germany. Zurich was the first city to take action against the Jewish community by voting never to admit Jews into thier city .

Laws were issued from Bern to the towns of Basel, Freiburg in Breisgau, and Strasbourg, to pursue the Jews as poisoners. All the Jews in Basel were closed in a wooden building, constructed for the purpose, and burned without sentence or trial. Soon after the same thing took place at Freiburg.
At Eslingen, the whole Jewish community burned themselves in their synagogue. Jews were executed in 1349, throughout Germany, Italy, and France, with impunity and in the eyes of the entire world.

The humanity and prudence of Clement VI must be mentioned to his honour. Pope Clement VI asked that gentiles treat Jews with tolerance. The Church had lost authority during the Plague, and now had few loyal followers. He protected the Jews at Avignon and also issued two bulls in which he declared them innocent. Several other princes and counts took the Jews under their protection.