He was ordained to the Priesthood on 24 October 1980 at the Cathedral of Saint Catherine of Alexandria, Dumaguete City, and was assigned by the Most Rev. Epifanio Surban, D.D., first Bishop of Dumaguete, to Saint Joseph Seminary as teacher, formator, principal, and academic dean at a time when the seminary was transitioning from a high school seminary to the college seminary that it is now.
During summers, Fr. Cortes continued his studies at the University of Santo Tomas and finished his Licentiate in Scared Theology and Master of Arts in Higher Religious Education. After several years in seminary formation work, he proceeded with advanced studies at the Angelicum University in Rome where he obtained a Doctorate in Scared Theology. This period of academic studies also enabled him to attend international courses such as “Fostering Human Religious Development” at the Gregorian University in Rome and “Bible and the Holy Land” at Saint George’s College in Jerusalem, Israel. Years later, he also attended a course on “Leadership in a Participatory Church” at the East Asian Pastoral Institute, Quezon City.
Presbyteral Ministry
Upon his return to the diocese, he was assigned by the Most Rev. Angel Lagdameo, D.D., second Bishop of Dumaguete, as rector of Saint Joseph Seminary and later appointed him Vicar General as well. He also became Parish Priest of the Heritage town of Bacong. When Bishop Lagdameo convoked the First Diocesan Synod of Dumaguete, he entrusted the task of presiding officer to Msgr. Cortes. These administrative functions in the diocese gave Msgr. Cortes an invaluable opportunity to be delegate to two historic ecclesial events in the Philippine Church, the Second Plenary Council of the Philippines and the National Pastoral Consultation on Church Renewal. When Bishop Lagdameo was promoted as Archbishop of Jaro, Msgr. Cortes became the Diocesan Administrator of Dumaguete until the arrival of the third Bishop of Dumaguete, the Most Rev. John Du, D.D.. A few months later, Pope John Paul II appointed Msgr. Cortes as Auxiliary Bishop of Cebu and Titular Bishop of . His Episcopal ordination was held at the Dumaguete Cathedral on 8 January 2002.
Episcopacy
Auxiliary Bishop
Bishop Cortes served as Auxiliary Bishop of Cebu as well as Parish Priest of Santo Rosario Parish from January 2002 until November 2013, for almost twelve years, allowing him vast pastoral experiences and opportunities under the tutelage of two Archbishops of Cebu, His Eminence, Ricardo J. Cardinal Vidal, D.D., and his successor, the Most Rev. Jose S. Palma, D.D. Aside from responsibilities in the Archdiocese of Cebu, Bishop Cortes also serve as chairman of CBCP Permanent Committee for the Cultural Heritage of the Church from 2007 to 2013, as well as being a member of two other Commissions.