The friars controlled the educational system during the Spanish times. They owned different schools, ranging from the primary level to the tertiary levels of education. The missionaries took charge in teaching, controlling and maintaining the rules and regulations imposed to the students.

These missionaries emphasized the teachings of the Catholic religion starting from the primary level to the tertiary level of education. The students in the primary level were taught the Christian Doctrines, the reading of Spanish books and a little of the natives' language. Science and Mathematics were not very much taught to the students even in the universities. Aside from the Christian Doctrines taught, Latin was also taught to the students instead of Spanish.

The schools before were exclusive for the Spaniards. The Filipinos were only able to enter the schoo.1 in the late 19th century. The schools also limited their accommodations to the sons of wealthy Filipino families in 1863.
Although the schools were already open for Filipinos, the friars still believed that the Filipinos would not be able to match their skills and that the only way for the Filipinos to learn fast was to impose upon them strict discipline which means applying corporal punishment.

The schools for boys and girls were separated. The first established schools were exclusive for the boys. The Augustinians built the first school in the Philippines situated in Cebu in 1565.

College was equivalent to a university during the Spanish regime. The student graduated with the degree in Bachelor of Arts (Bachiller en Artes). The first college school for the boys was the "Colegio de San Ignacio" which was established by the Jesuits in Manila in 1589. They also established the "Colegio de San Idelfonso" in Cebu in 1595. In 1601, "Colegio de San Jose" was established. Meanwhile, in 1589, the "Escuela Pia" was entrusted by the government to the Jesuits. Later, this was called Ateneo de Municipal which is now the famous Ateneo de Manila University.

The Dominicans also made a name as they established one of the best universities in the Philippines, the University of Santo Tomas, that was opened in 1611. In 1630, the Dominicans established another university, the "San Juan de Letran" for the orphaned boys.

"Colegio de Santa Potenciana" was the first school and college for girls. This was opened in 1589. Following the birth of the first school for women, Colegio de Santa Isabel opened in 1632. The religious congregations also established schools for the girls called "beaterio". The so-called "beaterio" was meant for orphaned girls who could not afford to educate themselves. The subjects taught were housekeeping, cooking, sewing and embroidery-making, and others intended for good housekeeping.

The effect of education to the Filipinos was only compelled to the friars' influences from their lessons based on the Christian Doctrines or teachings. Indeed, the friars were effective in evangelizing the Catholic religion to the Filipinos.

One major failure of the educational system of the religious congregations was the withholding of the Filipinos to learn other bodies of knowledge. Besides limiting education to the teaching of Spanish, Latin, and the Filipino languages, the teaching of Religion was also given emphasis. Thus, the teaching of Mathematics and Science were neglected.

In entirety, education during the Spanish regime was privileged only to Spanish students. The supposed Philippine education was only a means to remain in the Philippines as colonizers. For this reason, the Filipinos became followers to the Spaniards in their own country. Even auspicious Filipinos became cronies, to the extent that even their life styles were patterned from the Spaniards.

Meanwhile, several educated Filipinos referred to as ilustrados began movements directed towards change in the system of government in the Philippines. Despite their wealth and education, the ilustrados were still considered by the Spaniards to be inferior. One of the goals of the ilustrado was to be in the same level with the proud Spaniards. The growing number of ilustrados in the Philippines maybe considered one of the major effects of education by the Spaniards in the Philippines.

Philippine Information