He performed with Bob Dylan in concert in 1965, and in the recording studio in 1965 and 1966, including playing Hammond organ with Dylan at the (in)famous Newport Folk Festival of 1965. He worked extensively with Mike Bloomfield for a number of years after the two met as session musicians on Dylan's Highway 61 Revisited album. Kooper also played organ with Dylan during his 1981 world tour.
In 1965, he co-formed The Blues Project, although he left them shortly before their most famous gig at the Monterey Pop Festival in 1967. He formed Blood, Sweat & Tears in the same year, leaving after the group's first album, Child Is Father to the Man, in 1968.
Kooper played on hundreds of records, including The Rolling Stones, B. B. King, The Who and Cream. On occasion, he has even overdubbed on his own efforts, as on The Live Adventures of Mike Bloomfield and Al Kooper, as Roosevelt Gook. He discovered the band Lynyrd Skynyrd, and produced their first three albums, including the single, "Sweet Home Alabama" and the iconic "Free Bird". Kooper also wrote the score for the TV series Crime Story and the film "The Landlord" and has also written music for several made-for-television movies. Kooper also produced a now rare album by a group called Appaloosa. He was also the musical force behind many of the children's series "Banana Splits" pop tunes, including "You're the Lovin' End."
Kooper has published a memoir, Backstage Passes: Rock 'n' Roll Life In The Sixties (1977), now available in revised form as Backstage Passes & Backstabbing Bastards: Memoirs of a Rock 'N' Roll Survivor (1998). The latter includes indictments against manipulators within the music industry, including his one-time business manager, Stan Polley. His status as a published author enabled him to join (and act as musical director of) the Rock Bottom Remainders, a band made up of writers including Dave Barry, Stephen King, Amy Tan, Matt Groening and Scott Turow.
Kooper currently teaches songwriting and production at Berklee College of Music in Boston, and plays weekend concerts with his bands The ReKooperators and The Funky Faculty.
During the recording of "Like a Rolling Stone", Paul Griffin moved from organ to piano. Kooper told producer Tom Wilson that he had a good organ part for the song (which he later noted was just a ruse to get into the session), and Wilson responded "You're not an organ player, you're a guitar player", but Kooper insisted that he play. Before Wilson could explicitly reject Kooper, he got a phone call. Kooper went and sat down at the organ (a Hammond B3), though he had rarely played organ before the session. Wilson soon returned, surprised to find Kooper in the studio. Throughout the song the organ can be heard coming in just behind the other members of the band, as Kooper followed to make sure he was playing the right chords. During recording, Dylan famously said, "Turn the organ up," and a classic rock organ part was born. While the combination of piano and organ was common in church settings, it was relatively new to rock music and attracted considerable attention.