Founded and granted by royal charter from D. Sebastião in 1569, the Jesuits' College of Funchal held its first lessons the following year on the 6th of May, feast of St. John the Evangelist, who became the patron of the institution.

At the end of the sixteenth century, the college was transferred to its current location, quickly becoming one of the most important buildings on the Island of Madeira. It was built out of the island's stone and the first plan of the building was sent to Rome in 1575, to be reviewed and authorized by the authorities of the Society of Jesus.

For decades, the priests and laymen of the Society of Jesus' community in Madeira conducted religious and academic activities in several buildings spread across Funchal. Just few of these buildings remain unaltered by the years, yet it is certain that their characteristics did not please the Jesuits in any great fashion, leading them to a number of renovations of their property. The College of Funchal began to gain international importance when, beyond its usual religious and academic activities, it started to cater to the lodging and readying needs of the Jesuits who had been sailing to the New World, to found or integrate colleges and Jesuit communities throughout South America, Africa and Asia.

Many historical characters were directly linked to the College of St. John the Evangelist. Among them, there was Father Pedro da Fonseca (eminent Jesuit theologian and philosopher, dubbed the Portuguese Aristotle), who made corrections to the original plan of the building. Also king D. Carlos visited the college, when the building served as a barracks for the infantry. Finally, the presence of Portuguese armed forces is proved by Madeiran paving stone, decorated with the emblems of regiments that had been stationed there.

Although, it was a wealthy institution in the Jesuits' time, little remains of their estate that can be identified as such. The religious treasures and the considerable library of the time would be found serving the Diocesan Seminary, diluted into the Diocese's own estate. Through vague references, it is believed that a great deal of the Jesuit furniture was taken by the British or destroyed by time and use.

The present decoration of the College is directly linked with the history of the University of Madeira (UMa). It was intended, during its foundation, to install the rectory in Quinta do Monte, leaving the College for ground of classes and research. Thus, the furniture that once served the Austrian Imperial Family, during its exile in Funchal, was brought to the College for its decoration. Pieces from the Institute of Arts and Design of Madeira and the Superior School of Education of Madeira, institutions that merged with the UMa, were added to its estate, as well as assets acquired for their patrimonial value.

During the period, from the foundation of the Jesuits' college to the establishment of the rectory of UMa, many other institutions were housed in the complex, and almost all of them connected to education. From the public lectures during the reforms of the Marquis of Pombal to the Diocesan Seminary, through the Lyceum, the Gonçalves Zarco School, the Primary Magisterium and the Superior School of Education, all left their mark on the College, as well as the British and Portuguese regiments, the Military Band and the Agricultural Cooperative, which functioned here.