He is a recipient of the Gregori Aminoff Prize (2003), "for his pioneering development of methods to interpret electron density maps and to build models of biological macromolecules with the aid of computer graphics" and the Lindo Patterson Award, 2005, from the American Crystallographic Association.

Jones is most noted for development of widely used programs for fitting models into crystallographic electron density maps, first Frodo, then its further developed version O (molecular graphics), and for involvement in structure validation. He has solved a very large number of protein crystal structures and is listed as a depositor on 126 structures at the Protein Data Bank, especially emphasizing enzymes and viruses. Web of Science credits him with over 29,000 citations, and Google Scholar with over 14,000 citations (since 1990) and an h-index of 58, including over 11,000 citations for O and 1700 for Frodo. He is currently a professor at Uppsala University in Sweden.