The CIIMAR is a non-governmental and non-profit organization with individual and collective members (Institute of Biomedical Sciences Abel Salazar, Faculty of Sciences, Farmacy, Law and Engineering and University of Porto) that constitute the General Assembly. The associates elect a Board of Directors, composed of five elements, that supervises and defines the policy for scientific and technical activities and oversees the everyday management. The Centre has a Scientific Board, composed of all PhD members of the institution, which functions as an internal body with general responsibilities to advise and monitor the scientific and technical activities.

The organizational model of CIIMAR also includes an External Scientific Advisory Board that provides independent evaluation and advice on the scientific activity of the institution and is composed of three distinguished members of the international scientific community. The CIIMAR is also regularly evaluated by the Foundation for Science and Technology by means of international evaluation panels. The researchers are grouped into three main Research Lines, each with one coordinator. Each Research Line is subdivided into several Research Groups and these into Research Teams or Laboratories, which are headed by one principal investigator.

The CIIMAR established professional Supporting Offices Units and Technological Platforms Services that, under the supervision of the Board of Directors, provide daily support and develop essential actions, from purely administrative matters to those supportive of general use of research facilities and services.