Yonathan Mizrachi has an MA in archaeology from the Hebrew University of Jerusalem. Since 1998 he has been an active archaeologist in excavations of the Hebrew University, the Israel Antiquities Authority, and other organizations. Since 2005 he has participated in community excavations—a project of excavations conducted in conjunction with the local community, in which the community is an equal partner and has a say in deciding the future of the site once the excavation has ended. The project was conducted first in the Ir Ganim neighborhood in Jerusalem and then in other places. Since 2007 he has been writing on the connection between archaeology and the political conflict, with an emphasis on Jerusalem and the West Bank, and has been an activist in this area.
In 2009 he was one of the founders of Emek Shaveh, which deals with the place of archaeology in the political conflict and with aspects of heritage rights as part of human rights. Since the founding of Emek Shaveh he has been its managing director.
At the Van Leer Jerusalem Institute he heads, together with Prof. Chaim Noy, the Steering Committee for Creating a Policy Document Regarding the Preservation and Display of Jerusalem’s Antiquities.