When Bishop Godfrey Okoye died suddenly on 17 March 1977, a search for a worthy successor ensued. It eventually became apparent that Msgr. Michael Eneja, who had served as Rector of a Seminary, Vicar General of a prominent Archdiocese and a Spiritual Director in a Major Seminary, was the most qualified to fill the post. On 10 November 1977, Pope Paul VI, the man who was instrumental in the creation of Enugu Diocese in 1962, appointed him the third Bishop of Enugu.

His episcopal ordination took place on Sunday, 26 February 1978, at the Holy Ghost Cathedral, Enugu. The principal ordaining prelate was His Excellency, Most Rev. Dr. Jerome Prigione, Apostolic Pro-Nuncio to Nigeria.

His administration was characterised by humility and brotherly love, and he maintained an open-door policy throughout his episcopacy. There were no "High Tables" during meetings or gatherings of priests and religious. In the same vein, the Bishop's house was just like any other parish house where priests had free access. According to him, "Priests are not visitors or strangers in the Parish House [including his own]."

Sanctity and the necessity of acquiring it loomed large in all his homilies and public addresses. This is because, as he said, "It is sanctity (union) with God that is the whole aim of the struggle." As Bishop, he not only continued his ascetic lifestyle but also endeavoured to inculcate the same in priests and laypeople alike. In his view, "Self-denial is a sine-qua-none of good living."

Besides the insistence on holiness, especially for his priests, the Bishop also emphasised two other merits that priests must aspire to, namely studies and morals, which he also variously termed learning and character. During an all-priests meeting in 1995, the priests were given a curious assignment by His Lordship—to submit to him within 14 days their categorisation of the Enugu Presbyterium "with or without your names" in the areas of learning and character.

We must recall that within the Nigerian Bishops' Conference, Bishop Eneja chaired the Commission on the formation and quality training of the Pastoral Agents of Evangelization, namely, the Seminarians and Priests of Nigeria. The assignment given to his priests was, therefore, intended to vet his success in this important ecclesiastical function within his own Presbyterium. It would be interesting to know how the priests scored the Enugu Presbyterium. Still, it is common knowledge that further education for his priests was a primary concern in Eneja's episcopacy. He sent more priests for further studies in both national and international universities than any other bishop before and after him. He repeatedly reminded priests of the importance of continuing education.

He urged them to buy and read important ecclesiastical and secular literature, such as the Osservatore Romano (to which he was a regular subscriber), the writings of the Popes, national and international newspapers and magazines, etc. To ensure that priests acquired learning, he educated them; to enforce good character in them, he set up a three-man committee which he called "Eye of the Diocese". Their job was, among other things, to "examine what tampers with the good reputation of priests."

Under Bishop Eneja, the parishes grew exponentially. On 26 November 1990, Nsukka was excised from Enugu Diocese and made the Catholic Diocese of Nsukka with Most Rev. Francis Okobo as its first Bishop. His retirement was made public on 8 November 1996, and on 8 February 1997, he officially handed over to his successor, Most Rev. Dr. Anthony Okonkwo Gbuji.

Bishop Michael Eneja remained an active and well-respected shepherd of his flock. His books and Lenten pastorals are indicative of his own deep spiritual life, and his numerous public addresses and homilies bear witness to his popularity among all levels of society. Groups and individuals, fellow bishops and government officials flocked to him for advice. He was second to none in his use of Bible verses to buttress his exhortations, teachings and admonitions.

Bishop Eneja was endowed with good health even during his time as Bishop Emeritus. All the ill-health issues he went through at this time were those that are connected with old age. On 1 November 2008, he was admitted to the Niger Foundation Hospital, and two weeks later, on 14 November, he passed on in the Lord.

The funeral brochure of the late Bishop Eneja bore the telling Caption: "Exit of a Saint and a Generation." This captures the general perception of the people about the man Eneja. He exhibited the theological virtues of faith, hope and charity and the cardinal virtues of prudence, justice, fortitude and temperance in a manner that singled him out in all his ecclesiastical and social endeavours throughout his meritorious life as a seminarian, priest and Bishop.

His firm belief that he was a mere instrument in the hands of God was given expression in his episcopal coat of arms: Fiat Voluntas Tua (Your Will be done). Many think, and rightly so, that he represents a generation of the Nigerian clergy that are a class apart in their approach to the priesthood.