From its constitution in 1993 until 1998, the presidency of the Foundation was held by the Government of Navarre via the representation of its Minister for Education and Culture. After this initial stage, the presidency went on to be occupied by the Elder Hermit of the Brotherhood of Hermits of Arnotegui, or a person nominated by that entity.
The nine trustees that comprise the Board of the Mystery of Obanos Foundation are as follows:
- Ministry of Culture of the Government of Navarre.
- Archbishopric of Pamplona.
- Obanos City Council.
- Parish of San Juan Bautista of Obanos.
- Brotherhood of Hermits of Arnotegui.
- Association of Friends of the Way of St. James of Pamplona.
- Association of Friends of the Way of St. James of Estella.
- Two relevant members from the fields of Art and Culture of Navarre.