Along with disciplines of theology – such as exegesis of the Qur'an (tafsir) – the university taught fiqh (Islamic jurisprudence), Arabic grammar, history, science and medicine.

The manuscripts covered almost all subjects and sciences, including grammar, logic, documentations, etiquette of research, cosmology, arithmetic, geometry, minerals, vocational training, etc.

[2] Much of the library's original collection was dispersed or destroyed when the Spanish occupied Tunis and broke into the Zaytuna Mosque in 1534.

[1] The institution received greater attention and political patronage in the 18th century, attracting financial support from the ruling Husainid beys.

In 1896 new courses were introduced such as physics, political economy, and French, and in 1912 these reforms were extended to the university's other branches in Kairouan, Sousse, Tozeur, and Gafsa.

Some prominent members of the Algerian nationalist movement studied here, such as 'Abd al-Hamid ibn Badis, Tawfiq Madani, and Houari Boumédiène.

[citation needed] Reforms to the education system in 1958 and the creation of the University of Tunis in 1960 reduced the Zitouna's importance.

[2][7] For years afterward, under the rule of both Bourguiba and his successor Ben Ali, the educational institution was kept officially and physically distinct from the mosque itself.