He started his research career under the German occupation of Belgium. From 1940 onwards he gave clandestine lectures to students. In 1941, the university formally closed to protest the forced appointment of Flemish pro-Nazi New Order professors by the occupiers; he continued giving clandestine lectures until the Liberation of Belgium in 1944. During that time window he also published 21 articles. In 1943, Prigogine and his future wife Hélène Jofé were arrested by the Germans; after multiple interventions including by the Queen Elisabeth, they were eventually released a couple of weeks later.