Manuel was ordained a bishop on June 29, 1983, in the same year the St. Joseph the Worker Parish was elevated to a cathedral.

On November 21, 2015 Pope Francis appointed David William V. Antonio (then Auxiliary Bishop of Nueva Segovia) as apostolic administrator of the vicariate.

The third apostolic vicar, Pablito M. Tagura, was ordained as bishop at the diocesan shrine of Jesus the Divine Word, Christ the King Mission Seminary in Quezon City and was consecrated by Cardinal Luis Antonio G. Tagle, Prefect of the Discastery for the Evangelization of Peoples, Co-consecrated with Charles John C. Brown, Apsotolic Nuncio to the Philippines and Gilbert A. Garcera, Metropolitan Archbishop of Lipa on February 17, 2023.

Newly ordained Bishop Tagura was installed on February 25, 2023, at St. Joseph the Worker Cathedral, which was presided by Charles John C. Brown, the Apostolic Nuncio to the Philippines, together with the bishops in the Philippines, Society of the Divine Word and the San Jose clergy.

On July 1, 2023, the Apostolic Vicariate of San Jose celebrated its 40th anniversary with a Thanksgiving Mass was presided by Gilbert A. Garcera, Metropolitan Archbishop of Lipa.