Boychuk spent the next four years in the Avalanche organization playing primarily for their American Hockey League (AHL) affiliates.

[10] After initially making the Bruins opening night roster, Boychuk was primarily a healthy scratch in the first months of the season.

After returning from a conditioning assignment in Providence, he established himself within the Bruins as a two-way defenceman to finish with 15 points in 51 games to earn a two-year contract extension on June 24, 2010.

[12] The following season, Boychuk was rewarded with a three-year contract extension to remain a fixture on the Stanley Cup-winning Bruins blueline.

During the 2012–13 NHL lock-out, Boychuk ventured to Europe and signed a temporary contract in Austria with EC Red Bull Salzburg of the EBEL on November 16, 2012.

[17][18] On November 25, 2020, the Islanders announced that Boychuk would be retiring due to an eye injury that he suffered in a game against the Montreal Canadiens on March 3, 2020.