John Paul Jones is widely considered to be a highly influential and important bassist, keyboardist, and arranger in the history of rock music. Chris Dreja, the rhythm guitarist and bassist of The Yardbirds, has described him as "the best bass player in Europe".

Many music publications and magazines have ranked Jones among the best rock bassists of all time. He was named the best bassist on Creem Magazine's 1977 Reader Poll. In 2000, Guitar magazine ranked him third in the "Bassist of the Millennium" readers' poll.

Jones is currently part of the supergroup Them Crooked Vultures with Josh Homme (Queens of the Stone Age/Kyuss/Eagles of Death Metal) and Dave Grohl (Nirvana/Foo Fighters). The group released their first single "New Fang", and their debut, self-titled album in 2009.

In October 2010, John Paul Jones was awarded a "Gold Badge Award" by The British Academy of Songwriters, Composers and Authors for his outstanding contribution to Britain’s music and entertainment industry. On 10 November 2010, he was honored with the "Outstanding Contribution Award" at the Marshall Classic Rock Roll Of Honour Awards.