His manner of death is unclear. "The Times" of London and the Russian "Turkestan Gazette" both reported that he had died after a short illness. The contemporaneous historian Musa Sayrami (1836–1917) states that he was poisoned on May 30, 1877 in Korla by the former hakim (local city ruler) of Yarkand, Niyaz Hakim Beg, after the latter concluded a conspiracy agreement with the Qing (Chinese) forces in Jungaria. However, Niyaz Beg himself, in a letter to the Qing authorities, denied his involvement in the death of Yakub Beg, and claimed that the Kashgarian ruler committed suicide. Some say that he was killed in battle with the Chinese.