Cortez was ordained a priest on June 23, 1974. He initially served as a parochial vicar at the
Cathedral of San Pablo while also taking on the role of Prefect of Discipline at the Minor Seminary of San Pablo. From 1975 to 1978, he became the parish priest of Saint John the Evangelist Parish in
Kalayaan, Laguna. He later took on the role of chaplain at a public school in
Tondo, Manila, from 1979 to 1982. From 1983 to 1985, Cortez was assigned to pastoral ministry in
Venasque,
France. Upon returning to the Philippines, he served as a spiritual director at Saint Peter College Seminary in
San Pablo, Laguna from 1985 to 1986. His ministry in seminary formation continued when he was appointed spiritual director at the San Pablo Theological Formation House in
Tagaytay City from 1988 to 1990, and at Saint Peter's College Seminary in San Pablo City from 1993 to 1994. In 1993, he also took on the responsibility of being the parish priest at
Our Lady of Angels Parish in
Santa Maria, Laguna. He later served as spiritual director at Saint Peter's College Seminary again from 1995 to 1999 while being appointed director of the Office for the Formation of Priests in 1998. By 1999, Cortez became a member of the Synodal Examinators, the Presbyteral Council, and the College of Consultors. He was the parish priest at
Saint Therese of the Child Jesus inside
University of the Philippines Los Baños in
Los Baños, Laguna from 2000 to 2004. == Episcopal ministry ==