He continued to work on research projects until 2016 when he accepted an invitation to serve as a Program Director at the National Science Foundation (NSF) and co-lead the major funding multidisciplinary and multi-agency opportunity (Innovations at the Nexus of Food, Energy, and Water Systems, jointly funded by NSF and USDA-NIFA). While at NSF, he led the development of a new multidisciplinary research initiative called Signals in the Soil (SitS). He completed his responsibilities at NSF late in 2019, and he now works part time at the University of Florida on various initiatives locally, nationally, and internationally.

He developed a remarkable career based on mathematical modeling and computer simulation to integrate scientific knowledge from different disciplines for use in agricultural decision-making. His work has been acknowledged through his advanced rank at the university, through numerous awards and honors, and through the careers of many scientists he has trained. Dr. Jones was elected to the National Academy of Engineering in 2012.

Jones created a process that integrated models for several crops that he and his colleagues developed and models developed elsewhere that used different structures and data and reworked them so that they could all fit into a unified modeling scheme, effectively creating a standard framework for additional crops. He also added more components to the models, including soil fertility and pest management. This modular approach made it was relatively simple to extend the model framework to include more crops and to address more complex scenarios.