He became finance minister in the government of Chilean president Salvador Allende and then spent three years as a political prisoner (from September 11, 1973 to 1976) after the military coup of General Augusto Pinochet.

Subsequently, forced into exile after negotiations on his behalf by Amnesty International, he moved with his family to Palo Alto, California, and worked as a researcher in the Computer Science department at Stanford University.

Flores "had spent his prison years reading philosophy books smuggled in by friends and family, and emerged steeped in phenomenology, the study of the structures of experience and consciousness.

At Berkeley he developed his work on philosophy, coaching and workflow technology, influenced by Martin Heidegger, Humberto Maturana, John Austin and others.

His newest project is Pluralistic Networks Archived 2010-04-13 at the Wayback Machine, a professional development company dedicated to teaching skills and sensibilities enabling people to work together with others while navigating turbulent historical times.

After the coup d'état he was imprisoned, subjected to prolonged, systematic psychological torture and later driven to exile by the military regime of Augusto Pinochet.

[5] Prior to being appointed Finance Minister by Allende, Flores was responsible for launching and overseeing Project Cybersyn, "one of the most ambitious applications of cybernetics in history.