On October 12, 1944, as Romania signed an armistice with the United Nations, Manoilescu was jailed without trial for 14 months, during which time he was expelled from his position at the Polytechnic Institute. Because of the bad sanitary conditions in prison, he became sick with endemic typhus, and sent to the hospital for contagious diseases in Colentina. Set free in December 1945, he resumed work on his unfinished writings, and became an advocate of harvesting geothermal power in Romania (his innovations in the field were patented on the name of his son, Alexandru Manoilescu). He was once again jailed by Communist Romanian authorities on December 19, 1948, and was brought first to Jilava prison, and then to the prison of Ocnele Mari. While being held there, Manoilescu became, together with the philosopher Petre Ţuţea, a members of an "underground academy" organized by inmates.