The IBVF is managed by both personal and collegiate branches.
The personal government branches are constituted by the Director, Vice-Director and Secretary.

The collegiate governing branches are the Institute Board and the Scientific Senate.

The Institute Board consists of the following:
Director of the Institute
Vice-Director of the Institute
Secretary of the Institute
Research Groups Leaders
A representative of the CSIC research staff
A representative of the staff of the Department of Plant Biochemistry and Molecular Biology of the University of Sevilla
A number of representatives of non-staff research personnel
A representative of non-scientific staff

The Scientific Senate, chaired by the Director of the Institute, consists of the entire staff of the Institute holding PhD degrees.