In 1922 he was arrested for resisting the Bolshevik campaign to confiscate church valuables. The actual reason for the arrest is the rejection of the renovationist split. Together with Hieromartyr Archimandrite Sergius (Shein) (52 years old), Martyr John Kovsharov (lawyer, 44 years old) and Martyr Yuri Novitsky (Professor of St. Petersburg University, 40 years old), he was shot in the vicinity of Petrograd, presumably at the Rzhev firing range. Before the execution, all the martyrs were shaved and dressed in rags so that the executioners would not recognize the clergy.

At the time of his death, Metropolitan Veniamin was 45 years old.