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. Daddy Longhead retired after 10 years, leaving Pinkus free to explore other projects including Skinny Leonard and Areola 51. 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.
He currently appears with Honky and has in the past played weekly on Monday nights at the Jackalope, in Austin, Texas, with an assortment of other musicians called the Guit Down Syndrome.
Pinkus also performs with Pure Luck,who released a self-titled release in 2017 on Heavy Feather Records. He leaves his bass to play Banjo and Guitar in this project.
On their 30th anniversary tour in 2013, Pinkus joined the Melvins in place of Jared Warren (on paternity leave) as well as performing with the opening Honky. He subsequently joined the Melvins full-time, touring with them in 2014 in support of the album Hold It In, which also featured Butthole Surfers founder Paul Leary, and again in 2015. He also plays on the song "Captain Come Down" which was first released in 2015 on Chaos as Usual, a split release with Le Butcherettes, and later included on the 2016 album Basses Loaded.
In 2018, J.D. Pinkus released a solo album, "Keep on the Grass" on Cassette tape on Minner Bucket Records and Compact Disc on Heavy Feather Records. It was recorded entirely on banjo and features a rendition of the song "Bride of Crankenstein" from the Melvins album Hold It In. The C.D. release show is with Sleep in San Pedro on September 15th 2018.
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. Released on April 20, 2018, the aptly titled Pinkus Abortion Technician features both bass players and four songs written or co-written by Pinkus.