Timothy Onwuatuegwu took part in the 1966 military coup which overthrew Nigerian Prime Minister Abubakar Tafawa Balewa while also killing many other Northern generals. Onwuatuegwu was put in control of a small band of Igbo soldiers whose main job was to assassinate any Nigerian general they were able to catch in Lagos. Although the coup was stopped by the Igbo general Johnson Aguiyi-Ironsi both Onwuatuegwu and his superior Colonel Chukwuma Kaduna Nzeogwu were able to control the northern portion of Nigeria for a few weeks. Both Onwuatuegwu and Nzeogwu were arrested by Nigerian police officers in early February but were not executed which outraged many Northern civilians. For an entire year Onwuatuegwu was in an Enugu prison until May 30, 1967 when he was freed by Biafran president Odumegwu Ojukwu.
When Biafra was declared independent on May 30, 1967 Ojukwu made Onwuatuegwu a Major in his Army. Onwuatuegwu didn't see much action until Operation OAU in 1968 when he and Biafran Colonel E.A. Eutuk were put in charge of defending Owerri, Umuahia, and Aba. Onwuatuegwu fought against the forces of Nigerian General Benjamin Adekunle in May 1968 but lost the city to Murtala Muhammad's men on August 28, 1968. On July 18, 1968 Onwuatuegwu was able to capture the city of Umuahia from Benjamin Adekunle after many days of heavy fighting. On April 21, 1969 Onwuatuegwu assisted E.A. Eutuk's soldiers during the Defense of Umuahia in which Onwuatuegwu was able to drive off all Nigerian forces within a day of fighting. In January 1970 the Biafrans were on the edge of defeat and Onwuatuegwu escorted Biafran president, Odumegwu Ojukwu, to Uli Airport. Soon after Ojukwu fled to the Ivory Coast Nigerian general Olusegun Obasanjo invaded Uli and Onwuatuegwu was shot dead by Obasanjo's men as he planned to escape to Cameroun. Biafra had already surrendered to Nigeria before the death of Onwuatuegwu.