Malone, 45, first served as the Mets' strength and conditioning coach under Bobby Valentine in 2002, and later worked in the same capacity for the Royals (2000-01), Indians (2004-05) and Padres (2006-12).
An All-American defensive tackle at the University of Rochester, Malone regularly competes in organized weightlifting competitions. He has also worked as a football strength and conditioning coach at Rochester, Princeton University, Albright College and Columbia University.
Malone replaces Brad Andress, who was not retained after two seasons in the position.
Other than this turnover, the organization has made few noteworthy changes to its training staff since Sandy Alderson took over as general manager in October 2010. Head trainer Ray Ramirez has held his position for the past eight seasons.