Since its constitution in 1993, the presidency of the Foundation was held until 1998 by the Government of Navarra, in the person of its Minister of Education and Culture. After this first stage, the presidency passed to the Hermit Mayor of the Brotherhood of Hermits of Arnotegui or person appointed by it.

As of June 2023, a representative of the University of Navarra will join as a new trustee.

The ten trustees that make up the Board of the Misterio de Obanos Foundation are the following: