A chapel was situated within the grounds of the Collegio de S. Paulo, where, according to tradition, St. Francis is believed to have celebrated Mass. To the left of the chapel lies a well, said to be the place where the Saint washed his feet.
Tradition holds that this was the location where Xavier engaged in prayer, overwhelmed by fervor to the point of feeling suffocated. In this moment, he opened his cassock near his chest and exclaimed, "Satis est Domine, satis" (it is enough, Lord, enough), as he was consoled by celestial visions. It is said that this chapel was constructed to commemorate the site of this event. Here, he devoted many nights to prayer. Father Lancelot Xavier asserts that the saint himself requested the chapel's construction and celebrated Mass within its walls. Others contend that it was built in his honor posthumously. According to Francisco de Souza, the author of Oriente Conquistado, there were two chapels within the college grounds, dedicated to S. Antonio and S. Jeronimo, with the current chapel likely being one of them. It underwent repairs in 1859 and again in 1884. The chapel's walls were adorned with numerous paintings illustrating the life of the Saint, and by the end of the 17th century, it remained in good condition. However, as the city became deserted, the structure began to deteriorate. In 1627, the sanctuary, which included a small portico with seating on either side, a well, the facade, the choir loft, and a roofless nave, was still standing.
A tradition holds that the Saint planted several trees within the grounds of the College, including a jackfruit tree situated near the Chapel, whose bark was believed to cure various ailments. A traveler reported in 1595 that he observed two jackfruit trees and two mango trees in the garden of St. Paul's College, all attributed to the same saint. It is widely acknowledged that the tree adjacent to the chapel was highly valued by the Catholic community in Goa. Fragments of this tree and sculptures crafted from its wood were regarded with profound respect. The images sculpted from the wood of this jackfruit tree were particularly esteemed. In the Church of Santa Rita of Maina, Curtorim, there exists a crucifix that bears the following inscription on its reverse side: 'He Formada esta Cruz do lenho da jaqueira, que piantou 0 Glorioso S. Francisco Xavier Apostolo da India, junto da sua Capela no Colegio Velho do S. Paulo de Goa. Ano 1805'. This crucifix originally belonged to the Convent of S. Francisco de Assisi and was presented to the Chapel of Maina shortly after the expulsion of religious orders from Goa in 1835.