The lyrics of "So Long, Frank Lloyd Wright" have multiple meanings. On one level, the song praises the famous architect, who died in 1959. However, the lyrics also refer to the upcoming breakup of the Simon and Garfunkel duo. Art Garfunkel had studied to become an architect, so on this level the lyrics can be taken as a farewell from Paul Simon to his friend and partner Garfunkel like another song on Bridge Over Troubled Water, "The Only Living Boy in New York." While Garfunkel sings the song's fadeout to the words "so long," producer Roy Halee is heard on the recording calling out "So long already Artie!" Other lyrics of the song refer to the creative process, such as referring to the singer not having learned the tune and to the nights when the singer and Frank Lloyd Wright would "harmonize 'til dawn." The lyrics also refer to the singer thinking of Wright when looking for inspiration.
The accompaniment includes congas, strings, a flute and a guitar part played in bossa nova style, primarily using seventh chords. The song has a stately melody and the tune incorporates varied rhythms and syncopations. The song's key alternates between G-flat major and G major. Paul Simon has recalled that he had been listening to Brazilian music, probably Antônio Carlos Jobim, when he wrote the tune for "So Long, Frank Lloyd Wright." Author Walter Everett suggests that the repeating note section of the bridge about one minute into the song effectively suggests the ordinariness of other architects, and also suggests some of Wright's architectural signatures.
Garfunkel did not realise that Simon had intended the song to refer to their partnership until many years after the album had been released. In an interview he remarked that Simon "never let me in on that" secret. He added that "I find that a secretive and unpleasant thing to have done to you." However, he has come to terms with the song, as he states in the liner notes to his 2012 compilation The Singer, in which "So Long, Frank Lloyd Wright" was included, that he can ignore this subtext, since the song is "just so much fun to sing", and writes about Paul Simon that "one loves the giver of a beautiful gift".