[1] In 1990, he and Butthole Surfers' lead vocalist Gibby Haynes released Digital Dump, the only album from their psychedelic house music side project The Jackofficers.

Upon leaving Butthole Surfers, Pinkus worked full-time with the Austin trio Daddy Longhead, which he had assembled during his waning months in the band, and which included longtime Atlanta associate Jimbo Young on guitar and Rey Washam on drums.

Pinkus played with Helios Creed on his albums NUGG: The Transport and Activated Condition, and has also collaborated with Bad Livers frontman Danny Barnes several times in a live setting.

On February 12, 2018, the Melvins announced that Pinkus would be joining them, alongside current bassist Steven McDonald (Redd Kross), on their next album and subsequent tour.

On August 27, 2021, the band Tiny Tree released "XI" and JD Pinkus performed on the track titled "December" through the label Onama Media Group.