Harassed by the Iron Guard, which blacklisted him for assassination, Popa managed to survive its "National Legionary State" regime, proclaimed in September 1940. However, "Însemnări Ieșene" was banned, with some of its staff members moved to the fascist-inspired "Cetatea Moldovei" review. A Iași medical faculty purging commission, headed by Iron Guard men, proposed Popa's transfer "to another scientific institution", citing Popa's "left-wing ideas" as a rationale. Under the more lenient fascist dictatorship of Ion Antonescu, Popa continued to speak his mind, in particular objecting to Romania's participation in World War II alongside Nazi Germany. He was, as Boia notes, "an intransigent antifascist, [who] would naturally fit into any sort of plot against the regime". In 1942, following Rainer's retirement, he was transferred to Bucharest, where he worked as a professor for four years. After Rainer's death in 1944, he also took over the Anthropological Institute and reattached it to the medical school. While there, Popa wrote a study showing the lack of any scientific basis for Aryanism and asserting that there was no reason to oppress Jews. Traian Săvulescu, afraid to offend Antonescu, refused to publish it; Popa nevertheless read the work before the Academy in late 1943. The listeners, few of whom were pro-German, reacted positively. However, a January 1944 address was seen as a veiled attack on the dictator, to whom the members were largely sympathetic, and as a result drew a chillier reaction. One of his conferences at the Academy, "Reforma Spiritului. Știința ca bază de primenire a omului" ("Spiritual Reform. Science as a Basis for Bettering Mankind") objected to Romania's economic dependency, claiming that Romanians were at risk of falling back among "agricultural peoples", those "destined to perpetual ignorance". By that time, the security service, "Siguranța Statului", was keeping Popa under constant surveillance. In April 1944, together with other prominent intellectuals, Popa signed a petition asking Antonescu to seek peace with the Allies and end the war immediately. As noted by Boia, this "academics' memorandum" was belated, and did not expose its signers to any special persecution, since the Red Army was already poised to invade Romania.