On March 15, 1950, Kupriyanov was arrested and transferred to Moscow. He was imprisoned in Lefortovo Prison two days later. In October 1950, the investigation regarding Kupriyanov was finished and he was sentenced to capital punishment. However, Kupriyanov's execution was postponed due to Stalin's rejection of Malenkov's demand for execution. On January 17, 1952, the Military Collegium of the Supreme Court of the USSR sentenced Kupriyanov to 25 years of forced labor with confiscation of all property under Article 58. He was soon sent to the Intalag, but his sentence was changed in July 1952 to imprisonment. On August 18, his sentence was changed to 10 years of imprisonment without confiscation of property. His wife, Vera Vasilievna was sentenced to imprisonment for "not informing the authorities about her husband's sabotage". Kupriyanov's eldest son and daughter were exiled to Taraz, Kazakh SSR. After the death of Joseph Stalin in the spring of 1953, Kupriyanov's family was allowed to return to Leningrad.