On 2 February 1933, the Catholic Mission in Eastern Nigeria finally established a secondary school at Onitsha. With Father W. L. Brolley and two African teachers, a college section comprising thirty students was started in one of the dormitories of St. Charles Training College Onitsha. Later in the year, the college moved to its permanent site under the name Christ the King College.

Michael Eneja joined the establishment in 1939, as mentioned above, after it had become, in the words of Bishop Heerey, "a famous educational establishment." The academic excellence of Christ the King College Onitsha received its first official recognition in 1936 when it scored highest in all of Nigeria after the Cambridge Junior and Senior Examinations.

As a seminarian, Michael distinguished himself as a pious and law-abiding student. This did not escape the notice of his teachers, especially Father Reagan, who was the religion teacher and a mentor. His burning desire to be a priest never diminished throughout his seminary days. Thankfully, his parents did not raise any objections to his chosen vocation.

The Bishop recalls a question his mortally sick father posed to him: "Do you like any other thing in this world?" The answer, he says, was an emphatic "No." The only desire he had in the world was to be a priest of God, and after 49 years of service as a priest and Bishop, he says: "I am deeply grateful to God for showing me my vocation and fully supporting me with many graces and gifts."

His father died in 1942 just as he was preparing for his Senior Cambridge Examination that same year. With one essential source of financial support gone, God provided another in the form of sponsorship by a Polish-American benefactress named Rosalie Partensqui, who supported him financially for the rest of his seminary days. Between 1943 and 1944, Michael Eneja served the mission as a teacher at the College of Immaculate Conception C.I.C., Enugu, and after that, proceeded to the Major Seminary at Okpala in 1945.

Among his teachers at Okpala was Father, later Bishop, Joseph Whelan, who had the privilege of forming a unique set of Igbo clergy in the persons of Mark Unegbu, Anthony Nwedo, Michael Eneja, Godfrey Okoye and Stephen Ezeanya. All five later became bishops. Others include Moses Emeremnini, Clement Ulogu, Peter Meze, Vincent Madike, Edward Ahaji and John Ogbonna. Michael Eneja was in his final year of Theology when St. Paul's Major Seminary was transferred to Enugu in 1951.