Allen has spent most of his career in New York City, where he has played with Lester Bowie, George Cables, Betty Carter, Ron Carter, Jack DeJohnette, Frank Foster, Winard Harper, Butch Morris, David Murray, Wallace Roney, Cindy Blackman, Orrin Evans, Gerald Cleaver, Me'shell Ndegeocello, Dave Douglas and Nigel Kennedy.
Allen's debut album, In Search of J.D. Allen, was awarded the Best New Artist award in Italy in 1999. His next release, Pharaoh's Children, was named one of Jazziz magazine's Critics Pics Top 10 Albums of the Year. The Victory! album, released in 2011, received a four star rating in DownBeat and was ranked the third best jazz album of 2011 by NPR.