Since Sun Ra and John Gilmore died, Allen has led the Arkestra, and has recorded two albums as their bandleader. In May 2004, Allen celebrated his 80th birthday on stage with the Arkestra, as part of their performance at the Ninth Vision Festival in New York City. Allen gave other performances on his birthday in 2008 at Sullivan Hall and at Iridium Jazz Club in 2018, both in New York City.