In 1963, Motian left Evans' group to join up with Paul Bley for a year or so, and began a long association with Keith Jarrett in 1966, appearing with the pianist's American-based quartet through 1977. In addition, Motian freelanced for artists like Mose Allison, Charles Lloyd, Carla Bley, and Charlie Haden's Liberation Music Ensemble, and turned down the chance to be John Coltrane's second drummer.

In 1972, Motian recorded his first session as a leader, Conception Vessel, for ECM; he followed in 1974 with Tribute. He formed a regular working group in 1977 (which featured tenor Joe Lovano) and recorded several more dates for ECM, then revamped the ensemble to include guitarist Bill Frisell in 1980. Additional dates for ECM and Soul Note followed, and in 1988 Motian moved to JMT, where he recorded a long string of fine albums beginning with Monk in Motian. During the '90s, he also led an ensemble called the Electric Bebop Band, which featured saxophonist Joshua Redman, guitarists Kurt Rosenwinkel and Brad Shepik, and bassist Stomu Takeishi. In 1998, Motian signed on with the Winter & Winter label, where he began recording another steady stream of albums, including 2000 + One in 1999, Europe in 2001, and Holiday for Strings in 2002.

In 2005, Motian moved to the ECM label, releasing I Have the Room Above Her that same year, followed by Garden of Eden in 2006 and Time and Time Again in 2007. In 2009, he released his fifth in his series of standards albums with On Broadway, Vol. 5 and returned in 2010 with the trio album Lost in a Dream on ECM. The following year, Motian released several albums including Consort in Motion, his exploration of Renaissance and Baroque composers on Kind of Blue, the concert album Live at Birdland on ECM, and Windmills of Your Mind featuring guitarist Bill Frisell on Winter & Winter. A hugely influential drummer, bandleader, composer, and a journeyman live performer, Motian died from complications of myelodysplastic syndrome, a bone marrow disorder, early in the morning on November 22, 2011 in New York City. He was 80 years old. The album Further Explorations featuring pianist Chick Corea and bassist Eddie Gomez appeared posthumously on Concord in January, 2012.