He played the majority of the season with linemates Brad Boyes and newcomer Marco Sturm, who had been acquired in a trade that sent captain Joe Thornton to the San Jose Sharks in November 2005.

Then Bruins general manager Mike O'Connell recalled in a June 2011 interview that the organization had decided to build the team around Bergeron instead of Thornton, preferring the former's on- and off-ice character.

[12] Playing under a defensive system employed by new head coach Dave Lewis,[13] he recorded his second consecutive 70-point campaign in 2006–07 with 22 goals and 48 assists.

Checked from behind by Philadelphia Flyers defenceman Randy Jones, Bergeron hit his head on the end-boards, knocking him unconscious.

He lay motionless on the ice for several minutes before being wheeled off on a stretcher and taken to Massachusetts General Hospital, where he was diagnosed with a broken nose and a grade-three concussion.

[14] Bergeron made his first public statements regarding the injury on November 8, saying he would not take any legal action and that Jones had tried to contact him to apologize.

[15] On January 19, 2008, the Boston Globe reported Bergeron had been sent on vacation by then Bruins general manager Peter Chiarelli and that he would likely sit out for the remainder of the season as his recovery had regressed.

[16] In March 2008, Bergeron started preliminary on-ice practice with Bruins goaltender Manny Fernandez, who was himself recovering from knee surgery.

[17] He steadily progressed into full-contact practices in early-April, aiming for a playoff return against the Montreal Canadiens in the opening round; however, he was held back by team doctors.

[21] He returned to action with the Bruins for the team's preseason opening game on September 22, 2008, against the Montreal Canadiens, an 8–3 victory played in Halifax, Nova Scotia.

[22] After the 2008–09 season began, on October 23, Bergeron scored his first goal since his concussion, in a 4–2 home loss to the Toronto Maple Leafs.

[23] Two months later, in a game against the Carolina Hurricanes on December 20, Bergeron collided with opposing defenceman (and future Bruin) Dennis Seidenberg, suffering another concussion.

Halfway into the 2010–11 season, Bergeron scored his first career NHL hat-trick in a Bruins victory over the Ottawa Senators on January 11, 2011.

After the close of the 2012 playoffs, even with the defending Stanley Cup champion Bruins eliminated in the first round in seven games by the seventh-seeded Washington Capitals, Bergeron's constant defensive efforts on the ice earned him the Frank J. Selke Trophy as the NHL's top defensive forward for the 2011–12 season for the first time in his career.

[28] After finishing second in Selke Trophy voting for the lockout-shortened 2012–13 season (only behind Chicago Blackhawks forward and captain Jonathan Toews), Bergeron turned in a heroic playoff performance in the 2013 playoffs which included the tying- and game-winning goals against the fifth-seeded Toronto Maple Leafs in Game 7 of Round 1, and the overtime winner in Game 3 of the Eastern Conference Finals against the top-seeded Pittsburgh Penguins.

[47] On April 17, Bergeron was nominated for the Selke Trophy for an NHL-record eighth straight season which was eventually given to Ryan O'Reilly of the St. Louis Blues.

[51] At the end of the pandemic-shortened 2020–21 season, Bergeron ranked fourth on the Boston Bruins all-time scoring list with 917 total points (375 goals and 542 assists).

Just days before the June 9 elimination of the Bruins from the 2021 playoffs by the New York Islanders in six games in the second round, Bergeron was nominated as a candidate for the Frank J. Selke Trophy for the tenth straight season but the trophy was eventually given to Florida Panthers forward and captain Aleksander Barkov[52] - However, Bergeron would instead win the Mark Messier Leadership Award for the 2020–21 season; for strong team leadership, and contributions to the general society.

On that day, in a home game against the visiting Detroit Red Wings, Patrice scored only his second natural hat trick - and seventh hat trick overall - of his NHL career, as the foundation for a four-goal game by the Bruins team captain in a 5–1 defeat of the Red Wings.

He became the fourth Bruins player ever to score 400 goals for one team, joining Johnny Bucyk (545), Phil Esposito (459), and Rick Middleton (402).

With the season marking the end of Bergeron's contract, and in light of his age and history of injuries, there was considerable uncertainty as to whether he would continue with the team.

[58] Bergeron scored his 1,000th point in his NHL career on November 21, with an assist on a goal by longtime linemate Brad Marchand, in a 5–3 win over the Tampa Bay Lightning.

Bergeron helped the Bruins win the Presidents' Trophy as the best regular season team for 2022–23 before being defeated in 7 games in the first round of the 2023 playoffs by the eighth-seeded Florida Panthers after initially leading the series 3–1.

He finished the tournament with 5 goals and 8 assists totalling 13 points over 6 games while playing on a line with Sidney Crosby and Corey Perry.

[61] During the 2012–13 NHL lockout, Bergeron played for Lugano and competed for Canada at the 2012 Spengler Cup, along with teammate at the time, Tyler Seguin.