Born in Mississauga, Ontario, Manny Malhotra played for the local Reps in the MTHL before joining the Guelph Storm of the OHL in 1996-97. The next year he registered 51 points in 57 games for the club and helped them reach the Memorial Cup tournament. Malhotra was named to the tournament All-Star Team and won the George Parsons trophy as the Most Sportsmanlike Player at the Memorial Cup. That year he also played for Canada at the World Junior Championships and was was the seventh overall pick of the New York Rangers at the 1998 NHL Entry Draft.
During the 1998-99 season, Malhotra played 73 games as a rookie and went through the normal growing pains but did represent Canada at the 2000 World Junior Championships. His play tailed off the next season and he spent time in junior before joining the Rangers AHL affiliate in Hartford where he contributed to a Calder Cup championship. In 2000-01, Malhotra played most of the season in New York but struggled with his defensive play at times. He also played part of the year in Hartford but came to training camp in 2001 with the intention of staying in the NHL for the entire schedule.
Malhotra spent the entire 2001-02 season in the NHL, however, after 56 games with the Rangers he was traded to the Dallas Stars where he played up until the early stages of the 2003-04 season before being put on waivers and subsequently claimed by the Columbus Blue Jackets. Upon his arrival with Columbus the former first rounder went on to have his most productive season offensively, registering 25 points (12-13-25) in 56 games.
On July 1, 2010, Malhotra found himself an unrestricted free agent and signed a 3-year deal with the Vancouver Canucks.