Until 2003 he was Personnel Secretary to Joseph Cardinal Ratzinger (Pope Benedict XVI), the Prefect of Congregation for the Doctrine of the Faith. He was replaced by Monsignor Georg Gänswein. In February 2003 Msgr. Josef Clemens was appointed by Pope John Paul II Under-Secretary of the Congregation for Institutes of Consecrated Life and Societies of Apostolic Life. On January 6, 2004, he was ordained a bishop by Cardinal Ratzinger and appointed Titular Bishop of Segermes. Since November 2004 Clemens has been Secretary of the Pontifical Council for the Laity.
Josef Clemens was a member of the Organization-team of the XX. Weltjugendtag 2005 (World Youth Day) in Cologne.