Jones-Drew had a record-breaking season in 2009 for the Jaguars. In a 13-30 loss in Tennessee during Week 8, Jones-Drew rushed for 177 yards and two touchdowns on only 8 carries, one for 80 yards and another for 79 yards. This performance tied Hall of Famer Barry Sanders' record of rushing for two touchdowns in a single game of 75 yards or more, which was set by Sanders in a Week 7 game against the Tampa Bay Buccaneers in 1997. Jones-Drew became the third player to share the record, as San Francisco 49ers running back Frank Gore, also tied Sanders' record in a Week 2 game against the Seattle Seahawks during the same season.
Jones-Drew began the 2012 season by not attending organized team activities or training camp in hopes of signing a new contract with the Jaguars. Jones-Drew had two years remaining on a deal he signed in 2009, according to which his average salary was lower than that of fellow running backs Adrian Peterson, Chris Johnson, LeSean McCoy, Arian Foster, Steven Jackson, DeAngelo Williams, and Marshawn Lynch. There were rumors that he was open to being traded. After missing his team's entire offseason, Jones-Drew ended his holdout and reported to the team's facilities on September 2. He was placed on season-ending injured reserve on December 28, 2012.