In May 2001, Jones became director of the Victoria and Albert Museum. On his first day as director, he announced the scrapping of entry charges to the museum.[7] Under his directorship, a number of renewal projects have been completed, including the Medieval and Renaissance galleries which opened in 2009.[8]
On 18 November 2010, it was announced that Jones had been elected as the next master of St Cross College, Oxford; he took up the post in September 2011.[9] He retired from the post in September 2016, and was succeeded by Carole Souter.[10]
On 2 September 2023, it was announced that Jones had been named as interim director of the British Museum.[11]