The training of young scholars in the South is a very important objective of Sephis, as it clearly leads to capacity building at the academic level in the South. The organization of training workshops for young scholars is therefore also one of the strongest points of Sephis. Since 2004, 38 workshops have been organized with Sephis funding. Some of these workshops were organized by the Sephis centers and have become yearly activities, such as the Cultural Studies Workshop organized by CSSSC in Kolkata, India (in 2009 the 14th CSW took place); the Extended Workshop on Social History of CODESRIA in Dakar, Senegal (in 2009 the 5th Extended Workshop took place); and the Fabrica des Ideias of CEAO/UFBA in Salvador de Bahia, Brazil (in 2009 the 12th Fabrica took place). Since 2007, SEASREP in Manila, the Philippines, has organized the Alternative Research Methodology Workshop in October.

In addition to training workshops for young scholars, Sephis organizes workshops for senior academics, in particular mid rank scholars. These workshops can be organized by the Sephis centers, by the Steering Committee or by third parties. In general, a call for papers is distributed, sometimes as a hard copy and sometimes only digitally. The workshops mainly consist of presentations and discussion of papers, which, depending on the quality, are published afterwards in a special issue or as a book volume.