After the war, Martinon was appointed conductor of the Orchestre de la Société des Concerts du Conservatoire of Paris, and, in 1946, of the Bordeaux Philharmonic Orchestra. Other orchestras with which he was officially associated include the Chicago Symphony Orchestra as music director from 1963 to 1968; the Düsseldorfer Symphoniker, the French National Orchestra, the Israel Philharmonic Orchestra, the London Philharmonic Orchestra, the Radio Éireann Symphony Orchestra, the Concerts Lamoureux, and Het Residentie Orkest in The Hague.
Martinon's repertoire focused on the works of the early twentieth century French and Russian masters. The premieres of his violin- and cello-concerti were given by Henryk Szeryng and Pierre Fournier respectively.
Late in life, Martinon was diagnosed with bone cancer, not long after he guest conducted the San Francisco Symphony in their first complete performances of Deryck Cooke's orchestration of Gustav Mahler's tenth symphony.