May 1, 2007: Honored by the American Jewish Committee with its “Jan Karski Award” for his “efforts to identify the mass graves of Jewish victims of the Shoah” and “his dedication to furthering understanding between Christians and Jews.”
May 4, 2008: Rabbi David Ellenson awarded him the Roger E. Joseph Prize to Desbois in New York.
May 7, 2008: At the annual National Tribute Dinner, the Simon Wiesenthal Center in Los Angeles presented the Jewish Medal of Valor to Father Desbois for his commitment to religious tolerance and cooperation.
June 12, 2008: Received the Légion d’honneur for his work on the Holocaust.
October 9, 2008: Received the Shofar of Freedom Award.
May 12, 2009: Honorary doctorate from Bar Ilan University (Israel).
June 7, 2009: Honorary doctorate from the Hebrew University (Israel).
May 16, 2012: Honorary doctorate from New York University (United States).
May 3, 2013: Honorary doctorate from the University of Winnipeg (Canada).
March 4, 2014: Honored by the Representative Council of French Jewish Institutions (Conseil Représentatif des Institutions juives de France) with its Award.
May 21, 2015: honorary doctorate from the Jewish Theological Seminary of America.
April 28, 2017: honorary doctorate from the St. Francis College (United States).