Pope Francis accepted his resignation and appointed Bishop Mel Rey Uy, then the economer of the Diocese of Romblon, as his successor.

Furthering his education, he undertook postgraduate studies in theology at the Universidad Teológica del Norte de España in Burgos, Spain, and at the Angelicum University in Rome, Italy.

He also held the position of rector at St. Alphonsus School of Theology in Lucena City and served as a parish priest in Pagbilao, Quezon.

On December 15, 1984, Marquez was appointed as the first Bishop of the newly established Diocese of Gumaca and was consecrated on January 29, 1985, by Archbishop Bruno Torpigliani.

He was a staunch advocate of social justice and frequently spoke out against illegal gambling and human rights abuses in the province, calling on government officials to implement ethical leadership.