Kubelik's three years with the Chicago Symphony Orchestra, beginning in 1950, were frustrating. A persuasive rather than a dictatorial figure and a diplomat rather than a martinet, he lacked the ability to control the orchestra. Additionally, Kubelik's musical sensibilities had been shaped in the early twentieth century rather than the late nineteenth, as had been the case with his immediate predecessors, and he programmed far too much modern music for the taste of critics and subscribers. Kubelik was fortunate that his appointment coincided with the orchestra making its first move into long-playing records for the Mercury label. Among his two dozen recordings with the Chicago Symphony Orchestra was a riveting performance of Mussorgsky's Pictures at an Exhibition and one of Smetana's My Fatherland. Ultimately the fit just wasn't right between Kubelik and the orchestra, and he gave up the appointment. Kubelik served for three years, from 1955 through 1958, as music director of the Covent Garden Opera in London, where he conducted the British premieres of Janácek's Jenufa and Berlioz's Les troyens. From 1961 until 1979, he was music director of the Bavarian Radio Symphony in Munich, with which he also recorded extensively (for Deutsche Grammophon), and was the principal conductor of the Metropolitan Opera in New York during the 1973-1974 season as well. He was a most-welcomed guest conductor in Chicago on many occasions throughout his later career, appeared with virtually all of the world's major orchestras, and recorded extensively in England, America, and Germany. In 1973, he became a Swiss citizen. Rafael Kubelik embodied a tradition of robust post-Romantic music-making that was ideally suited to the recording medium as well as the concert hall. He was celebrated as a master of rich orchestral color, which was brought out most vividly in the late Romantic and post-Romantic scores for which he was most popular. This included much of the Russian repertory and virtually all of the nationalist music of the era, especially the work of his fellow countrymen Antonin Dvorák, Leos Janácek, and Bedrich Smetana. He recorded the latter's Má Vlast at least four times on as many different labels, the last at a live performance in Prague during 1990 at a concert commemorating the liberation of the country from Communist rule released on the Supraphon label. The sheer number of his recordings that remain in print, and their equal distribution between the "historical" and modern sections of classical music departments, speaks volumes about his enduring popularity and the validity of his performances and interpretations. His complete Beethoven and Mahler cycles remained in print for many years. Although relatively little of his operatic work was preserved on record, the small number of these are also well-regarded, especially his Rigoletto.
With the fall of the Communist dictatorship, Kubelik, who had been intermittently ill for several years, returned to Czechoslovakia for the first time in four decades with the intention of resuming composing full-time. As it was, he had authored five operas, several symphonies, and various works for soloist and orchestra, vocal works, and chamber pieces.