The Directorate of Academic Affairs is responsible for the connection between the administrative sector of the University with the academic one as well as for the provision of administrative support to the academic units (faculties, departments) with respect to various upcoming academic and research issues.
The Directorate is structured along the following Departments.
a)    Department of Undergraduate Studies and Student Care in Komotini
The Department of Undergraduate Studies and Student Care coordinates the Academic Departments for the uniform application of the provisions of the existing law related to the compilation of Curricula. It ensures that all curricula be gathered and that all amendments decided upon and effected be monitored. It is responsible for the timely preparation of all Departmental Study Guides and for the circulation of university textbooks. It oversees and coordinates the educational process throughout all Departments, and more specifically, it deals with issues arising in the timetable and the examination procedure. It is responsible for issues related to student registrations, transfer and placement exams for graduates coming from other higher education institutions who wish to study in one of the University’s department in the city of Komotini. It provides information to all interested parties with respect to issues of studies and research, coordinates healthcare issues as well as issues related to free food and accommodation, student trips, loans, scholarships, etc. It further forwards the decisions made by the academic units it supervises.   
b)    Department of Graduate Studies and Research in Komotini
The Department of Graduate Studies and Research provides guidelines to Academic Departments for the organization and operation of graduate programs of studies and scientific research programs. It forwards proposals for the approval of Graduate Programs of Studies and ensures for the receipt of the Senate’s approval of the submitted proposals and for the smooth running of all Graduate Programs.
c)    Departments of Academic Affairs in Xanthi and Alexandroupolis
The Departments of Academic Affairs in both Xanthi and Alexandroupolis have as their main objective the provision of administrative support to the academic and research issues of the academic units that reside in Xanthi and Alexandroupolis respectively. More specifically, the two Departments have the following responsibilities: they coordinate the Academic Departments that reside in the two cities and ensures the uniform application of the Curricula. They ensure that all curricula be gathered and that all amendments decided upon and effected be monitored. They are responsible for the timely preparation of all Departmental Study Guides so that they can be available to students upon their arrival at the beginning of each academic year. They are responsible for the circulation of university textbooks. They oversee and coordinate the educational process throughout all Departments, and more specifically, they deal with issues arising in the timetable and the examination procedure. They forward to the Central Directorate of Academic Affairs all proposals considering the approval of Graduate Programs of Studies. They are responsible for issues related to student registrations, transfer and placement exams for graduates coming from other higher education institutions who wish to study in one of the University’s department in the cities of Xanthi and Alexandroupolis. They coordinate healthcare issues as well as issues related to free food and accommodation, student trips, loans, scholarships, etc. and they further forward the decisions made by the academic units they supervise.