The cloister of San Agustin conforms to the design found in Europe as well as the Americas prevalent during the colonial period. The four corridors in the cloister have at each corner ornately carved baroque retablos with reliefs/paintings of saints believed to have been added in the 18th century. Here, processions as well as the friars used to pass and stop for prayers and rituals.

One of the most elegant woodwork in the entire church must be the exquisite pulpit located at the corner of the transept and nave, epistle side of the church. The intricacies of the carvings, its uniqueness and age alone are worthy of mention. Commissioned in 1627, it cost 2, 413 pesos

The four chapels at the gospel side of the San Agustin Church is shown and described.

The four chapels at the epistle side of the San Agustin Church is shown and described.

The Chapel of Legazpi was originally dedicated to St. Faustus which was sold in 1594 as the final resting place of Sargento Mayor Juan de Morones and his family. On the other hand, the remains of Legazpi and that of Juan de Salcedo were already interred here. During the British invasion of 1762, the various tombs were despoiled in search of hidden treasure. When the Augustinians returned a year later, they gathered some of the bones scattered in the various chapels and placed it in one common tombstone.

There are more than a dozen chapels inside the church of San Agustin with altars from various periods and architectural styles (baroque and neoclassical) with dedicatees varying over time depending on their patrons and changes done by the friars.