After guitarist Tim Agnello left Exodus in 1981, Holt joined the band and has been the main songwriter and the most senior member of the group ever since. Following Kirk Hammett's 1983 departure from Exodus to join Metallica, Holt kept the band going and for many years, he and Rick Hunolt were referred to as the Exodus' "H-Team" guitar players. Holt is the only member of Exodus who has played on every album.
On February 12, 2011, it was announced that Holt would be temporarily filling in for Jeff Hanneman in the band Slayer. Holt also played with Slayer for the Big 4 Concert in Indio California on April 23, 2011, as well as Fun Fun Fun Fest in Austin, Texas on November 6, 2011. Holt is still touring with Slayer and agreed to fill in after Jeff Hanneman died on May 2, 2013. He also recorded guitar tracks on Slayer's 2015 album Repentless, but did not have any writing contributions on the album, except for guitar solos.
In October 2008, Holt released an instructional guitar video called "A Lesson in Guitar Violence". He also produced Warbringer's second album, Waking into Nightmares.