During his 18-year career, he played as a centre for the Montreal Canadiens, Carolina Hurricanes, Vancouver Canucks, San Jose Sharks, Columbus Blue Jackets, Dallas Stars and the New York Rangers.

He joined the NHL after a two-year career in the Ontario Hockey League (OHL) with the Guelph Storm, where he served as captain in his final year.

During this time he was assigned on numerous occasions to the team's AHL affiliate, the Hartford Wolf Pack, with whom he won a Calder Cup championship in 2000.

Serving as team captain at the 2000 World Junior Championships, Malhotra led Canada to a bronze medal.

Earning a berth into the 1998 Memorial Cup, Guelph made it to the final, where they lost to the Portland Winter Hawks 4–3 in overtime.

[11] He was named to the Memorial Cup All-Star Team and was awarded the George Parsons Trophy as the tournament's most sportsmanlike player.

The Rangers scouted him as a strong, physical player with good hockey sense and character, comparing him to Adam Graves.

[15] The night before the deadline, Malhotra and the Rangers agreed to a three-year deal worth the rookie-maximum of $975,000 with performance-based incentives that could have increased his salary to $2 million.

[17] It was reported that Canucks general manager Brian Burke had requested Malhotra to be involved in a trade that would have sent him along with Niklas Sundström, Dan Cloutier and the Rangers' first-round pick in the 1999 draft in exchange for Bure.

[18] Rangers head coach John Muckler publicly declared before the beginning of Malhotra's second NHL campaign that he would be nothing more than a career third-liner.

[21] He was then sent for a two-week conditioning assignment with the Rangers' American Hockey League (AHL) affiliate, the Hartford Wolf Pack.

Upon his junior club's first-round playoff elimination, he was reassigned to the Wolf Pack where he recorded 1 goal and 6 points over 12 games to finish the regular season.

[19] Fifty-six games into his 2001–02 season with the Rangers, Sather dealt Malhotra to the Dallas Stars at the trade deadline, along with winger Barrett Heisten, in exchange for forwards Martin Ručinský and Roman Lyashenko.

He initially signed with HDD Olimpija Ljubljana of Slovenia on October 8, 2004, and recorded 27 points over 26 games (including both Slovenian league and inter-league play).

[12] Late in the 2007–08 season, on March 17, 2008, he recorded a career-high three points in one game (two goals and an assist) in a 4–3 win against the Detroit Red Wings.

As Columbus was plagued with numerous injuries over the course of the season, Malhotra was used on various lines while also in a shutdown role, playing against top opposing forwards.

After failing to sign with an NHL team, Malhotra accepted an invitation to the San Jose Sharks' training camp on September 17, 2009.

[2] On the first day of free agency on July 1, 2010, Malhotra signed a three-year, $7.5 million deal with the Vancouver Canucks that included a no-trade clause.

His success as a defensive specialist earned him early consideration for the Frank J. Selke Trophy as the league's best two-way forward.

[36] Limited to 72 games, Malhotra recorded his third consecutive 30-point season with 11 goals and 19 assists while playing on the Canucks' third line alongside Raffi Torres and Jannik Hansen.

In the midst of his recovery, Malhotra made an appearance during the team's pre-game ceremony at Rogers Arena, co-accepting the trophy with captain Henrik Sedin.

[41] By the end of the month, he was cleared by doctors to play in the Stanley Cup Finals against the Boston Bruins after missing the first three rounds against the Chicago Blackhawks, Nashville Predators and San Jose Sharks, respectively.

[notes 2] Canucks head coach Alain Vigneault assessed Malhotra during the season as "not the same physical player he was before",[44] adding, "He's still contributing but not maybe to the degree that he was before he got injured.

Near the end of the campaign, Malhotra was chosen as the Canucks' nominee for the Bill Masterton Trophy, an annual NHL award for perseverance, sportsmanship and dedication to hockey.

[45] With a diminished offensive role, Malhotra finished his second season in Vancouver with seven goals and 11 assists and 18 points in 78 games, as well as a –10 plus-minus rating while the Canucks as a team won their second consecutive Presidents' Trophy.

Fearing for his long-term health, Canucks general manager Mike Gillis took him out of the lineup for the season, a decision that he described as the "hardest thing [he has] done in [his] job".

After being unsigned by an NHL team at the start of the 2013–14 season and looking to continue his playing career Malhotra signed a 25-game professional try out (PTO) contract with the AHL's Charlotte Checkers.

[50][51] As a measure of the amount of respect he has earned in the locker room in just a few weeks, Manny was selected to be an interim assistant captain while Tim Gleason was out with an injury.

[citation needed] After Gleason was traded to the Toronto Maple Leafs, Malhotra was officially named an alternate captain for the remainder of the season.

Two months into the 2015–16 season, Malhotra returned within the Columbus Blue Jackets organization by signing a professional try-out contract with American Hockey League affiliate, the Lake Erie Monsters on December 3, 2015.