 His contract was not renewed by the Blue Jackets in the 2009 off-season and he became an unrestricted free agent. After failing to sign with an NHL team, Malhotra accepted an invitation to the San Jose Sharks'training camp on September 17, 2009. Five days later, he signed a one-year, $ 700,000 deal with the team. He went on to record a career-high 14 goals and plus-17 rating, along with 19 assists for 33 points, in his only season with the Sharks. He centred the team's third line and earned time playing wing on the powerplay. The Sharks did not re-sign him, however, and he became an unrestricted free agent for the second consecutive summer on July 1, 2010. Looking back on his time in San Jose, Malhotra called it the "most enjoyable season [he's] had as a pro," being able to play for a winning team and have a long playoff run for the first time in his NHL career.
