Rubin served most of his prison term in solitary confinement, during which he continued his research as best as he could. When he fell ill with a suspected cancer, he was removed to a hospital and encouraged to make further confessions in return for favourable treatment, but declined the offer. He was released on a commuted sentence in 1934 and allowed to work in Aktyubinsk, Kazakh SSR as an economic planner. Rubin was arrested once more during the Great Purge in 19 November 1937. After this arrest he was never seen alive again. He was executed under the accusation of Trotskyist conspiracy in 25 November 1937