IBIMA has entrusted its management to FIMABIS (Andalusian Public Foundation for Research in Biomedicine and Health of Malaga), an entity linked to the Regional and Virgen de la Victoria University Hospitals in Malaga and belonging to the network of research management foundations of the Andalusian Public Health System.

The management units are shared between IBIMA and FIMABIS and are under the direction of the Scientific Director and Managing Director of IBIMA. With regard to economic issues and management of IBIMA, these depend functionally on the Managing Director.