He received episcopal consecration on 6 January 1996 from John Paul II himself, with Archbishops Giovanni Battista Re and Jorge María Mejía serving as co-consecrators.

[1] When a group of Swiss intellectuals and theologians called for John Paul's resignation on 20 May 2004, on the occasion of his 84th birthday, Koch described it as "disgusting and disloyal".

[3][4] On 27 June 2007, Koch, along with several other Catholic prelates, attended a briefing from the Cardinal Secretary of State, Tarcisio Bertone, at the Apostolic Palace on Pope Benedict XVI's forthcoming allowing wider celebration of the Tridentine Mass.

Pope Benedict XVI announced the appointment of Koch as president of the Pontifical Council for Promoting Christian Unity on 1 July 2010, taking over from Cardinal Walter Kasper.

It is a great joy for me because ecumenism has always been in my heart since in my country, Switzerland, Protestants are very close to us and I have also had a particular interest in the Orthodox Churches.

"[9] On 16 October 2010, Pope Benedict appointed Koch as a member of the Congregation for the Doctrine of the Faith for a five-year renewable term.

The speech followed Koch's participation in a meeting of the doctrinal congregation to examine the latest progress in the Vatican's reconciliation talks with the traditionalist Society of Saint Pius X.

[13] 16 May 2012, Koch gave the Pope John Paul II Lecture on Interreligious Understanding at the Pontifical University of Saint Thomas Aquinas (Angelicum).