The MISS program is designed as a class-based course with a standard period of study of two years, if pursued full-time. It begins with a six-month preparatory phase containing the modules "Introduction to Intelligence and Security Studies", "Human Rights and Security" and "Digitalization". The aim of the preparatory phase is to introduce primarily students from the Bundeswehr with no in-depth knowledge of the work of intelligence services and military intelligence to the subject and to ensure a common knowledge base.

The preparatory phase is followed by the module "Theoretical Approaches and Methods of Intelligence and Security Studies" and two core study phases, each lasting three months. The core study phases cover five main subject areas in which students learn about the role of intelligence services in the political decision-making process, various intelligence-gathering methods, the development of peace and security in a changing world, communication and leadership in intelligence services, and the requirements placed on intelligence in the information age. Following this, students choose one of four possible areas of study, in which they can deepen the knowledge and methods they have acquired with a future professional assignment in mind. The areas of study they can choose from are "Cyber Defence", "Intelligence Services and Public Security", "Counterterrorism" and "Regional Security", each of which lasts three months. This phase is followed by a Master's thesis. The courses are held in Berlin, Munich and Brühl.