While at Southern Cross Catholic College, Jones used to train at the Redcliffe club in Scarborough, Queensland, and was coached by Ken Wood. Her training partners included fellow Australian team members, Geoff Huegill and Jessicah Schipper. After her disappointing campaign in Athens, Jones moved to train at the Fortitude Valley Pool in Brisbane, Australia, alongside Libby Lenton, under Swiss-born coach Stephan Widmar at the Commercial Swimming Club. Following the move, Jones began to speak openly about the depression and self-esteem issues that had plagued her following her being thrust into the spotlight at such a young age. The successes that followed endeared her to an Australian public that had been critical of her attitude following her failure to capture individual gold in Athens. Some, including Dawn Fraser, believed Jones had acted immaturely and ungratefully, particularly in her indifferent displays of emotion during post-race interviews and medal ceremonies.
In 2009, Jones became the new face of the World Animal Protection Australia & New Zealand anti-whaling campaign.
Jones confirmed her retirement from swimming in November 2012. She is planning to begin a university degree in psychology in 2013.
In 2015, Jones published an autobiography titled Body Lengths.