On August 31, 1940, while he was saying mass in St. Alexander's Church in Călăraşi, NKVD officers broke in and attempted to arrest him. Baltagă refused, saying he would follow them only after the mass. The political police had to retreat empty-handed. The following night, they snatched him from his bed, and without allowing him to dress, took him to Chișinău, where he was subjected to interrogation in the cellars of the NKVD building. His interrogator was NKVD lieutenant Cherepanov, a superior interrogator of the NKVD of the MSSR, who accused Alexandru Baltagă that "[...] in 1918, having an enemy attitude toward the Soviet Russia, he actively participated in Sfatul Țării, and voted for the estrangement of Bessarabia from Soviet Russia and for its Union with Romania [...] In the following year, as an active cleric, he fought against the revolutionary movement [...]" There exist reports that during his interrogation, Baltagă was subjected to physical and psychological pressure. It is reported that to investigators' questions "Show us your God!", he replied, "When you show me your mind, then I [would] show you my God!" (literal translation). After the Romanian Army crossed back into Bessarabia in early July 1941, the Soviets moved him to the interior of the USSR. He died what some Orthodox texts refer to as a martyr's death in Kazan on August 7, 1941.