In 1790 the archbishop of Manila ordered the parish church of Batangas to give one of its old, dismantled retablos to San Jose.

Manuel Blanco in 1812 replaced the original buildings with new ones made of masonry, he constructed the convento and began the work on the present church, but left in 1816 without seeing it completed.

Fray Bruno Laredo (1870–1884) improved both church and convent, rebuilding the bamboo sacristy in stone, and commencing the work on the transept.

Victoriano Perez (1890 to 1896) restored the L-shaped convent and completed works on the transept and dome.

[3] In 1911 there were no more Filipino priests available in San Jose; hence, a Capuchin friar was called to administer the parish.

From July 1911 to 1915, the Missionaries of the Sacred Heart stayed in San Jose, where they set up a small major seminary.

Luis was also responsible for the setting up the communion rails and lowering the windows for better light and ventilation.

The leaking roof was repaired, the windows lowered for more ventilation, the altar area and communion rails redecorated, and new murals painted.

In 2000, the parish retook possession of the convent, which had long been used by the Cursillo movement as a venue for its retreats.

Rony Alkonga OSJ began the much-needed repair on the roof and ceiling as well as a redesigning of the area to accommodate, among others, a parish museum.

Joey Apin OSJ as parish priest, the church of San Jose was proclaimed by Archbishop Gaudencio Rosales as an archdiocesan shrine.