The comedian took aim at Tom Cruise during the show making a comment about the alleged disappearance of Shelly Miscavige — wife of Scientology leader David Miscavige.
The 35-year-old comedian was the first Black host of the ceremony, taking to the stage at the Beverly Hilton on Tuesday, and received acclaim for his performance.
During the ceremony, Carmichael emerged with three statuettes and suggested that these were the awards Cruise returned to the Hollywood Foreign Press Association (HFPA) during last year's row about lack of diversity in the organisation.
He said: "Backstage I found these. [It’s the] three Golden Globe awards that Tom Cruise returned.
"I’m just a host briefly, or whatever, but I have a pitch I think. Maybe we take these three things and exchange them for the safe return of Shelly Miscavige."
Mrs Miscavige has not been seen publicly since 2007 and actor Leah Remini – who has been outspoken about her since she left the controversial religion in 2013 – has filed a missing persons report for Miscavige.
In 2018, the Church of Scientology described Remini as "a foaming anti-Scientologist" and said Mrs Miscavige "has personally and repeatedly told law enforcement that Remini's acts are abusive", choosing to live a private life.
Remini said last year that Cruise's deep connection to Scientology shouldn't be forgotten amid the praise for his work in Top Gun: Maverick — one of last year's highest-grossing movies.
Cruise was converted to Scientology by his first wife Mimi Rogers in 1986 and has since become arguably the most prominent public advocate for the religion.
Remini shared a clip of Carmichael's joke on Twitter, thanking the comedian for speaking publicly about the mystery around Mrs Miscavige.
Carmichael took aim at the Golden Globes' controversy during his monologue, opening the show by stating: "I am your host Jerrod Carmichael and I'll tell you why I'm here I'm here... because I'm Black."
He concluded his monologue by saying: "Regardless of whatever the Hollywood Foreign Press Association’s past may be, this is an evening where we get to celebrate.
"And I think this industry deserves evenings like these. And I’m happy you all are here. And I hope you have some fun tonight."
Viewers lauded Carmichael's performance on social media, with praise for his frank comments about the HFPA, as well as the reference to Scientology.
The Fabelmans and The Banshees of Inisherin were the big film winners on the night, winning the two Best Picture prizes.
Steven Spielberg also won Best Director for the former, while the latter won Best Screenplay and Best Actor - Musical or Comedy for Colin Farrell.
Multiverse-based thrill ride Everything Everywhere All at Once was also awarded, with acting prizes for stars Michelle Yeoh and Ke Huy Quan.
In the TV categories, it was House of the Dragon, Abbott Elementary and The White Lotus that ruled the roost, while Zendaya won an acting prize for her work on Euphoria.
Watch: Jerrod Carmicheal references HFPA race controversy in monologue