Shaw then founded the 42-voice Robert Shaw Chorale, perhaps the first full-time professional choir in the U.S. unconnected with a religious institution. Meanwhile he studied music theory, piano, and conducting technique. For eighteen years the Chorale toured incessantly and made many successful recordings, including some well-loved arrangements of Christmas favorites. In 1953 he accepted a position conducting mainly light music with the San Diego Symphony. In 1956 George Szell invited Shaw to build a chorus to match the standards of his Cleveland Orchestra, rapidly on the rise. Shaw accepted the post, and in the process also took formal and informal lessons with Szell. In 1966 the Atlanta Symphony Orchestra invited Shaw to become its next music director. During twenty years at its helm he built its quality and reputation to high international levels. When he took over in 1967, Atlanta was still essentially a segregated city. In his first year, Shaw established a week-long residency for the orchestra at Spelman College, one of Atlanta's historically black colleges. He also frequently conducted in the city's churches, black and white. In 1972 he gave the world premiere of Scott Joplin's opera, Treemonisha.
When Shaw's first five-year contract was up, the orchestra board voted not to renew his appointment because of the large quantity of twentieth century music he played, citing poor ticket sales. Within two weeks, however, 3,500 new subscribers sent in season-ticket checks, all bearing the notation that they were contingent on Shaw remaining the conductor.
Shaw was an extremely tough conductor. He raged, especially at the chorus members. He posted a formal letter after every choral rehearsal, chiding the singers and exhorting them onward. Koussevitzky once said he was "amazed that any group of adults would willingly endure such tyrannical treatment from a conductor." Shaw and the orchestra recorded for the Telarc label. He retired from the Atlanta podium in 1988 and was proclaimed conductor laureate, continuing to conduct regularly. He also made numerous guest appearances as a conductor, appearing in his signature midnight blue rather than black tails. Shaw spent four months a year in the village of Dordogne, France, where he conducted the Robert Shaw Institute and festival, sponsored by The Ohio State University.
Shaw died in 1999 of a massive stroke suffered while he attended a play directed by his youngest son. During his career he won thirteen Grammy awards and the 1991 Kennedy Center Honors.