From 2010 onwards, he served as the parish priest at St. Michael the Archangel Parish, Jagna, Bohol, while also pursuing further studies in Moral Theology at the San Carlos Major Seminary in Cebu City. In 2012, he served as Episcopal Vicar for the clergy of the Diocese of Talibon.
On February 14, 2016, he was appointed the Bishop of Tagbilaran by Pope Francis. His episcopal ordination took place on April 14, 2016, with the principal consecrator being Cardinal Luis Antonio Tagle, Archbishop of Manila, and co-consecrators being the Archbishop of Cebu, Jose Palma, and the Bishop of Talibon, Leonardo Y. Medroso. As Bishop of Tagbilaran, he worked to strengthen the pastoral and spiritual life of the diocese, focusing on enhancing the formation of the clergy and promoting Catholic education.
On July 16, 2025, he was appointed the fifth metropolitan Archbishop of Cebu, following the retirement of Archbishop Jose Palma on March 19, 2025. Archbishop Uy was installed as Archbishop of Cebu on September 30, 2025, at the Cebu Metropolitan Cathedral.