BIOFISIKA is a joint Research Centre between the UPV/EHU and the CSIC that is also supported by the FBB. This triage of Institutions provides a complementary core body essential for the functionality of the Centre and for warranting the successful achievement of the previous and future objectives.

The governance and organisational structure has different levels, all centred on the Scientific Director, which is selected by the General Council (GC) (composed by all researchers of BIOFISIKA), supervised by the University and CSIC for proper management strategies and supported by FBB, an Executive Board (EB), an international Scientific Advisory Board (SAB) and a Business Advisory Board (BAB)