He is best known for his work in the 1960s with artists such as Bob Dylan, Frank Zappa and the Mothers of Invention, Simon & Garfunkel, the Velvet Underground, Cecil Taylor, Sun Ra, Eddie Harris, Nico, Eric Burdon and the Animals, the Blues Project, the Clancy Brothers and Tommy Makem, and others.

Transition also released the first sessions led by Doug Watkins, Donald Byrd, and Herb Pomeroy.

[6] As a staff producer at Columbia Records, Wilson was one of the "midwives" of folk-rock, producing three of Bob Dylan's key 1960s albums: The Times They Are a-Changin', Another Side of Bob Dylan, and Bringing It All Back Home, along with the 1965 single, "Like a Rolling Stone.

[8] Wilson produced Simon & Garfunkel's 1964 debut LP Wednesday Morning, 3 A.M. which included "The Sound of Silence".

Seizing on local radio interest in the song in Florida and inspired by the huge success of the Byrds' folk-rock version of Dylan's "Mr Tambourine Man", Wilson took the duo's original acoustic track and, without Simon's or Garfunkel's knowledge, overdubbed electric instruments, turning the track into a #1 pop hit, helping to launch the folk-rock genre.

In 1966, Wilson signed the Mothers of Invention to Verve Records and was credited as producer on the group's debut album Freak Out!

Wilson also produced the Velvet Underground, featuring Lou Reed and John Cale.

Wilson resigned from MGM Records (then owner of Verve) prior to the release of White Light/White Heat and did not work with the Velvet Underground thereafter.

[12] Frank Zappa spoke highly of Wilson, who produced the Mothers of Invention's debut album Freak Out!

[2] Wilson appears as a minor character (portrayed by Eric Berryman) in the 2024 Bob Dylan biographical film A Complete Unknown.