Romania entered World War II in 1941, and Puiu served as Metropolitan of occupied Transnistria at Odessa from 16 November 1942 to 14 December 1943. There, he reopened churches closed by the Soviet authorities, helped the needy, the poor and children, and educated people in the Orthodox faith. He disregarded the ongoing extermination of the Jews in the region by the Romanian authorities. In August 1944, he was in Zagreb (present-day Croatia) for the ordination of an Orthodox bishop there, accompanied by a handful of Romanian priests. He sent the priests back to Romania, sure they would be safe, but decided to flee to the west, fearing punishment from the Soviets for his wartime religious activity in Transnistria. Indeed, a People's Tribunal, the Romanian counterpart of the Nuremberg military tribunals, sentenced him to death "in absentia" for war crimes on 21 February 1946.