In 2001, Baker guest-starred in That ’70s Show in season 3’s “Backstage Pass” as a janitor at the Ted Nugent concert. In November 2011, Baker released the song “2 Be Simple” with an accompanying music video which features Baker (credited as “Black Hugh Hefner”) in a bath robe dancing with scantily clad women. “For reasons that remain unclear,” wrote Jan Chaney of The Washington Post, “Baker has released … a track destined to be the party anthem at all your yuletide throwdowns.” Cameron Matthews called the song’s hook “infectious” with lyrics that “totally [capture] the daydreams of a middle-aged man in crisis.”

He was part of the Office cast which won Screen Actors Guild Awards in the Outstanding Performance by an Ensemble in a Comedy Series category in 2007 and 2008.

In December 2017, after several former Office actors expressed interest in a revival of the series, The Hollywood Reporter’s Lesley Goldberg said of Baker, “Why wouldn’t he return?!” After The Office ended in 2013, The Hollywood Reporter said that Baker has had few roles; Bustle said that he was “plenty busy with his other creative pursuits”. In July 2020, Baker launched a Kickstarter campaign to fund the production of a pilot for Uncle Stan, a proposed spin-off series of The Office focusing on Stanley as he moves to Los Angeles, California to help his widowed nephew Lucky run his failing motorcycle repair/flower shop.

Baker appeared in Raven’s Home as Principal Wentworth; previously, he had small parts in Scorpion and Life in Pieces. He appeared on the CMT series Still the King and in the films Captain Underpants: The First Epic Movie (2017), in a voice role, and The Happytime Murders (2018). He also appeared in a January 2018 advertisement for FileMaker Inc., a subsidiary of Apple Inc., as a farmer alongside former Office actors Paul Lieberstein and Kate Flannery. In 2020 Baker starred in a series of commercials for Honey Nut Cheerios.