The movement of SS Peter and Paul Seminary Okpala from Owerri Imo State to Enugu in 1951 made late Bishop Eneja one of the pioneers of Bigard – Enugu. At that time, Michael was already in his fourth year of theology. He was the first to receive the major orders in Bigard Chapel. On 29 July 1951, he was ordained a priest at Holy Trinity Cathedral, Onitsha, by His Grace, Most Rev. Dr. Charles Heerey, C.S.Sp. He thus became the first man in the old Nsukka Division to become a Catholic priest.

The following day, 30 July 1951, he said his 'First Mass', which was, in fact, a Mass of his reception by his people at St. Theresa's Catholic Church (now St Theresa's Cathedral) Nsukka. Fr. Michael Aluma, who attended the 'First Mass' as a minor seminarian, said that Fr. Eneja's reception was the most astounding event for the entire Nsukka and Wawa people who had not witnessed priestly ordination before then.

In those days, newly ordained priests were still students in the seminary. So, the young priest Michael Eneja returned to Bigard after the reception to complete his theological education the same year.

After completing his theological studies, he was very effectively schooled into the ministry by four eminent priests under whom he served as a curate: Rev. Fr. D.O. O'Keefe, C.S.Sp. at James parish, Aku in Nsukka area, from January to March 1952, Rev. Fr. (later Bishop) G.M.P. Okoye at St. Michael's Parish, Awgu, from April to September 1952, Rev. Fr. Mc'Grane, C.S.Sp., from September, 1952 to January 1953, Rev. Fr. (later Bishop) John Cross Anyogu at St. Patrick, Ogbete, from January 1953 to January, 1955. In all, his service as curate lasted for three full years, namely, from January 1952 - January 1955.

With the establishment of a new parish at Iva-Valley in January 1955, which was an outpost of St. Patrick's Ogbete, Fr. Eneja was made the pioneer parish priest. He remained resident at Ogbete, from where he administered his new parish effectively, the long-distance notwithstanding. It was only after a year, in 1956, that he became resident at Iva-Valley. The new parish had already spread into several outstations, including Abakpa-Nike, Agbogazi, Ako-Nike, Emene, Mburuiyiukwu, Neke-Uno, Ugwogo-Nike, Oruku, Owo, as well as the Reformatory at the Ngwo Hill-top.

With all these towns and villages attached to Iva-Valley parish, the young parish priest had an onerous task. He administered all these areas with great fervour and spiritual unction. He was also credited with constructing the present Iva-Valley Primary School, which the government took over but has now returned to the Catholic Church. He served the parish until October 1960, when Nigeria basked in the euphoria of independence from colonial rule. After that, he was sent to Rome to do a diploma course in Spiritual and Social Development.

When Fr. Godfrey Okoye was appointed Bishop of Port Harcourt in 1961, Fr. Michael Eneja was chosen to replace him as Rector of All Hallows Seminary Onitsha. All Hallows Seminary at the time was in a transition period with many attendant problems—the change of authority from missionary to local, the explosion in the number of students about five times above the original intake. Added to these challenges that faced the new Rector were the provision of qualified teachers, the upgrading of academic standards and physical structures of the institution. Until his death, his humility overwhelmed those working under him. As Rector, for instance, Michael Eneja would sneak out in the night to fetch water for the common use of his fellow priests in the rectory.

In 1961, he also succeeded Father Okoye as Chaplain of the defunct Eastern Nigerian Catholic Council (E.N.C.C.). Among other things, he transformed the E.N.C.C. from being a merely militant organ charged with the protection of Catholic educational and political interest in the Eastern Region to being an apostolic outfit that was also interested in converting its members for the Lord. His description of the organisation is, in fact, the outcome of his endeavours:

The spirit of sacrifice is what made the members different from other societies. They came to work for Christ, and they were prepared for whatever difficulties they might face in that work. When someone becomes a real member of the E.N.C.C., he has come to suffer for Christ. He is not afraid of difficulties. He also encouraged and supported the training of resource persons for liturgical apostolate – Catholic students, teachers, seminarians, postulants, and priests. This interest in training liturgical personnel would reach a climactic point when he became the bishop of Enugu.

In 1965, he became the parish priest of Immaculate Heart parish, Fegge-Onitsha. Here, he 'popularised the zonal system by which the parish was divided into zones for effective organisation of the laity.' This administrative structure has already been appropriated in the province. Michael Eneja's administrative acumen included his ability to visit the homes of his parishioners; he had personal knowledge of a significant percentage of the members of the parish. His interest in administration was tied with apostolic zeal – to bring all souls under his care to the Lord.

Fr. Michael Eneja was a real pastor, and his mission in Fegge abundantly revealed this vocation. He left Fegge at the outbreak of the Nigerian Civil War and the consequent evacuation of Onitsha in 1967. During the war years 1967-1970, he worked with fatherly tenderness to war-stricken Igbo people. St Charles Parish Achina in Awka area was his base. An informant, Msgr. Iloanusi remembers how, from Achina, Michael covered the entire area as far as Akokwa on foot, saying Masses for the communities and administering the Sacraments to their sick.

With the end of the war in 1970, Msgr. Michael Eneja came back to Fegge, but after a short stay, he was appointed Spiritual Director of Bigard Memorial Seminary Enugu, where he also taught Spiritual and Ascetical Theology. As a spiritual director in Bigard, Msgr. Eneja laboured to bring back the lost spirit of the old Igbariam Seminary. As a result, he reproduced his saintly life in most of his seminarians, who became priests. He left Bigard in 1976 for Sabbatical leave and later was posted to Christ the King Parish Onitsha, where he worked until he was elected bishop of Enugu.