Soon after leaving Fitzgerald, Flanagan played solo piano in New York. In 1979 he was a guest on the first series of Marian McPartland's "Piano Jazz" radio programs. He continued to work with other players, including as a trio with Tal Farlow and Red Mitchell in 1980. For much of the 1980s he led a trio that featured bassist George Mraz and various drummers. By around 1990 Flanagan was concentrating on his own appearances and recordings rather than sideman activities. In the early 1990s Mraz was replaced by Peter Washington, whose heavier bass lines added urgency to the trio's sound.