Following the German invasion of Poland, which started World War II in September 1939, the "SS-Totenkopf-Standarte Brandenburg" entered the town to commit various crimes against the population. Already in late September 1939, the Germans murdered Polish hostages from Kłodawa in the nearby Rzuchów forest, and one of the pre-war mayors, Władysław Zalewski, was murdered in November 1939 in Środa Wielkopolska. During the occupation by Nazi Germany, the town was renamed "Tonningen" (1940–1945). Already in 1940, the Polish underground resistance movement was formed in the town, and also secret Polish schooling was organized. In 1941, more than 1,500 Kłodawan Jews were killed by the Nazi Germans in the Chełmno extermination camp. In 1943, the Germans arrested some of the local Polish resistance members, who were then either sentenced to death or prison. The Kłodawa parish priest, Father Teofil Choynowski, was killed in the Dachau concentration camp in 1943. Kłodawa was eventually liberated on January 19, 1945 by the Red Army, and restored to Poland.