On the day of the January 1966 coup d'état, Katsina — a Major serving as the commander of the Kaduna-based 1st Reconnaissance Squadron — received reports of gunfire at the home of Premier of Northern Nigeria Ahmadu Bello.

Unaware that Bello had already been killed by Major Chukwuma Kaduna Nzeogwu's putschist group, Katsina ordered Corporal John Nanzip Shagaya and Sergeant Dantsoho Mohammed on a reconnaissance mission into the city where they found Bello's dead police guard along with the corpses of Brigadier Samuel Ademulegun and his wife.

[4] Within a few days, the coup was successfully repressed and General Officer Commanding Johnson Aguiyi-Ironsi took power as the first military Head of State.

[12] Tensions based on the Unification Decree, grief from the murders of northern leaders in the January failed coup, anti-Igbo conspiracy theories, and other sources rose greatly as misinformation spread across the North rapidly, forcing Katsina to embark on a tour to debunk false rumours that Aguiyi-Ironsi had barred Muslims from making the Hajj.

[13] Although a member of the government, Katsina echoed the growing anger felt by low-level Northern soldiers, using a speech to vow revenge for deaths in the January coup.

[14] After months of rising tensions, a mutiny in Abeokuta rapidly led to the July counter-coup that killed Aguiyi-Ironsi and scores of southern soldiers.

Katsina became renowned for conciliatory acts like stopping the 1 October mutiny of the 5th battalion in Kano before driving through the city with the Emir personally stopping massacres and looting; additionally, Katsina organized the smuggling of surviving southern officers (including future President Olusegun Obasanjo and his aide-de-camp Lieutenant Chris Ugokwe) to safety.

Key figures in his government included Ibrahim Dasuki; who later became Sultan of Sokoto, Ali Akilu; who later played a prominent role in the creation of states in Nigeria, and Sunday Awoniyi.

However, as Siollun notes, Ojukwu came to the conference extremely prepared for the crucial constitutional talks and successfully pushed the SMC to make massive concessions.

In this position, he led the war effort by doubling the size of troops, blockading of supplies to Biafra, and utilised air support from the United Arab Republic.