The teaching offered to students in Manila was very advanced, as will be seen from the following Syllabus of Education in the Municipal Athenæum of the Jesuits:—
| Agriculture. | Geometry. | Philosophy. |
| Algebra. | Greek. | Physics and Chemistry. |
| Arithmetic. | History. | Rhetoric and Poetry. |
| Commerce. | Latin. | Spanish Classics. |
| Geography. | Mechanics. | Spanish Composition. |
| English. | Natural History. | Topography. |
| French. | Painting. | Trigonometry. |
In the highest Girlsʼ School—the Santa Isabel College—the following was the curriculum, viz.:—
| Arithmetic. | Geology. | Philippine History. |
| Drawing. | Geometry. | Physics. |
| Dress-cutting. | History of Spain. | Reading. |
| French. | Music. | Sacred History. |
| Geography. | Needlework. | Spanish Grammar. |
There were also (for girls) the Colleges of Santa Catalina, Santa Rosa, La Concordia, the Municipal School, etc. A few were sent to the Italian Convent in Hong-Kong.
A college known as Saint Thomasʼ was founded in Manila by Fray Miguel de Benavides, third Archbishop of Manila, between the years 1603 and 1610. He contributed to it his library and ₱ 1,000, to which was added a donation by the Bishop of Nueva Segovia of ₱ 3,000 and his library. In 1620 it already had professors and masters under Government auspices. It received three Papal Briefs for 10 years each, permitting students to graduate in Philosophy and Theology. It was then raised to the status of a University in the time of Philip IV. by Papal Bull of November 20, 1645. The first rector of Saint Thomasʼ University was Fray Martin Real de la Cruz. In the meantime, the Jesuitsʼ University had been established. Until 1645 it was the only place of learning superior to primary education, and conferred degrees. The Saint Thomasʼ University (under the direction of Dominican friars) now disputed the Jesuitsʼ privilege to confer degrees, claiming for themselves exclusive right by Papal Bull. A lawsuit followed, and the Supreme Court of Manila decided in favour of Saint Thomasʼ. The Jesuits appealed to the King against this decision. The Supreme Council of the Indies was consulted, and revoked the decision of the Manila Supreme Court, so that the two Universities continued to give degrees until the Jesuits were expelled from the Colony in 1768. From 1785 Saint Thomasʼ University was styled the “Royal University,” and was declared to rank equally with the Peninsular Universities.
There were also the Dominican College of San Juan de Letran, founded in the middle of the 17th century, the Jesuit Normal School, the Convent of Mercy for Orphan Students, and the College of Saint Joseph. This last was founded in 1601, under the direction of the Jesuits. King Philip V. gave it the title of “Royal College,” and allowed an escutcheon to be erected over the entrance. The same king endowed three professorial chairs with ₱ 10,000 each. Latterly it was governed by the Rector of the University, whilst the administration was confided to a licentiate in pharmacy.
At the time of the Spanish evacuation, therefore, the only university in the City of Manila was that of Saint Thomas, which was empowered to issue diplomas of licentiate in law, theology, medicine, and pharmacy to all successful candidates, and to confer degrees of LL.D. The public investiture was presided over by the Rector of the University, a Dominican friar; and the speeches preceding and following the ceremony, which was semi-religious, were made in the Spanish language.
In connection with this institution there was the modern Saint Thomasʼ College for preparing students for the University.