Chapel of the Immaculate Concepcion – originally dedicated to Sta. Lucia then to Sta. Monica, it was only in the 19th century that this was dedicated to the Immaculate Concepcion. The baroque retablo was commissioned in 1754. The builder of San Agustin church, Juan Macias and his family are said to be interred here.
Chapel of Sta. Clara de Montefalco – this chapel was originally dedicated to San Juan de Sahagun then to the Holy Trinity. Later, in the late 19th century, it was dedicated to Sta. Rita. then at around 1922 – 1930 the image of St. Rita was transferred to the transept chapel and this was dedicated to the present saint. This retablo was commissioned in 1755 and serves as the final resting place of several Roxas family members.
Chapel of St. Joseph – the retablo was done in the 1750s, similar to the four other baroque retablos in the adjoining chapels. It is said that the last Spanish Governor General drew up the terms of the capitulation of Manila to the American here on 12 August 1898.
Chapel of the Assumption – Before it was renovated before World War II, the old retablo was said to be the same as that in the former Chapel of St. Augustine.
This chapel was acquired by the Roxas, Soriano and the Zobel families in the year 1893 that serves the final resting place of some of the old families distinguished members.