Later appointments included Grade Three staff officer Nigeria Army School of Infantry, Jaji, Director of Cadets, Nigerian Defence Academy, Director of the Armed Forces Command and Staff College, Jaji, Brigade Commander, 9 Mechanised Infantry Brigade, Military Secretary, Army Headquarters, and General Officer Commanding;1st Mechanised Infantry Division[3] Under the Military government of General Ibrahim Babangida, Shagaya was Federal Minister of Internal Affairs, a member of the Armed Forces Ruling Council and a member of the Police Council.

[3] Shagaya was appointed Field Commander in the ECOMOG Peacekeeping Force in Liberia in September 1993, relieving Major General Tunji Olurin.

[3] Shagaya was a founding member of the United Nigeria People's Party (UNPP), running unsuccessfully for the Senatorial seat of Plateau South in 1999 elections.

[8] Shagaya had converted from a military officer to a politician, earned the title of a moderate,[9] and was elected as Senator for Plateau South in April 2007, running on the platform of PDP.

[11] In an interview in October 2009 he defended the various military interventions since Nigeria gained independence, and stated that the influence of generals in politics since 1999 simply reflected their training and discipline.