Vancouver Canucks (2010–2013)
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. Malhotra was named an alternate captain during away games for the Canucks before the season began. He scored his first goal as a Canuck on October 22, during a 5–1 win against the Minnesota Wild.
Malhotra settled into the Canucks' lineup as the team's third-line centre, often playing with wingers Raffi Torres and Jannik Hansen, while playing significant time on the penalty kill and matching up against opposing team's best forwards. His success as a defensive specialist earned him early consideration for the Frank J. Selke Trophy as the league's best two-way forward. In an article on the NHL's website, he was chosen as the front-runner for the award at the mid-way point of the campaign. He was also credited with allowing the team to use centre Ryan Kesler in a more offensive role (Kesler was the team's previous shutdown centre); as a result, the second-line centre recorded career-highs in goals and points.
During a game against the Colorado Avalanche on March 16, 2011, Malhotra was struck in the eye by a deflected puck from Avalanche defenseman Erik Johnson. He immediately left the ice and underwent eye surgery the following day. It was announced on March 21, that Malhotra would not be returning to the lineup for the rest of the regular season and the playoffs, without further comment on Malhotra's condition. Eight days later, he underwent a second successful surgery on his eye.
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. His 61.7% faceoff percentage ranked second in the league behind David Steckel. The campaign also included the 100th goal of his NHL career, scored in a 3–0 win against the Anaheim Ducks on March 6, 2011.
On a team basis, Malhotra's first season with the Canucks saw them earn the Presidents' Trophy for having the best regular season record in the league. 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. Despite original statements from the team that he would not return for the playoffs, Malhotra began to gradually work his way up from light practices with the team in May 2011. 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.
Though he remained out of the lineup for Game 1, he returned for Game 2 and played the rest of the series as the team's fourth-line centre (late-season acquisition Maxim Lapierre filled in for Malhotra on the third line), with the Canucks ultimately falling to the Bruins with a 4-0 loss in game 7 of the series. Malhotra's regular season performance earned him six first-place votes out of 125 for the Selke Trophy. He ranked fifth in balloting, as teammate Ryan Kesler won the distinction at the year-end awards ceremony.
Malhotra struggled in 2011–12 due to having lost a significant amount of vision in his eye from his eye injury towards the end of the previous season. He was supplanted as the Canucks' third-line centre by rookie Cody Hodgson and later Samuel Påhlsson. Canucks head coach Alain Vigneault assessed Malhotra during the season as "not the same physical player he was before", adding, "He's still contributing but not maybe to the degree that he was before he got injured." Playing left wing on the fourth line, he remained an integral part of the team by playing on the penalty kill and taking important defensive zone faceoffs.
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. 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. However, he remained among the league's elite in terms of faceoffs, ranking fourth with a 58.5% winning percentage.
Continuing to struggle with his eye injury, Malhotra was put on the injured reserve a month into the 2012–13 season. 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". Malhotra had appeared in nine games without recording a point.