On 10 June 2019, he was detained and taken into custody the same day on charges of organising the activities of a terrorist organisation. In February 2020, Omerov was charged with preparation for violent overthrow of the constitutional order. On 12 January 2021, he was sentenced to 13 years in a strict regime colony. In October 2023, the court ruled that the Federal Penitentiary Service had incorrectly calculated Omerov's time in prison: according to the defence's calculations, he should have been transferred to the colony back in May. In prison, where Omerov was sent to serve the first years of his sentence, he started having problems with his eyesight. There is no ophthalmologist in the prison, so the Crimean Tatar cannot receive qualified medical assistance.