The CCI regularly engages in cooperative research projects with faculty at the University of Cape Town, and international researchers and research institutes. A number of such projects have been completed.

In 2014 the CCI, The Centre for African Studies (UCT), and the Tombouctou Manuscripts Project (Huma, UCT) embarked on a project to investigate the structural connection between Muslim religious authority and practices of knowledge transmission in Africa. Through the lenses of social and intellectual history, the project has looked at the activities of Chadian Muslim religious leaders as those of intellectuals who operate within a religiously sanctioned universe of ideas for the transmission and the on-going reconfiguration of a cumulative corpus of doctrines and practices.

In September 2013, the CCI, the Tombouctou Manuscripts project (HUMA), the Centre for the Study of Manuscript Cultures (University of Hamburg), and the French Cultural Institute of South Africa collaborated to host an international conference on Muslim manuscript cultures in sub-Saharan Africa. Many of the articles presented at the conference will appear in a collection that will be published by De Gruyter in September 2017.