Since 2001, Zinner has many collaborative efforts under his belt with such acts as TV on the Radio, Har Mar Superstar, Ronnie Spector The Horrors, and Scarlett Johansson. He contributed guitar and keyboard to several tracks on Bright Eyes' 2005 album Digital Ash in a Digital Urn and went on tour with the band as part of the rotating roster.

In 2005 Zinner formed a band Head Wound City along with members from The Locust and The Blood Brothers.

Zinner produced the re-mix of the track 'Compliments' on British group Bloc Party's 2005 album Silent Alarm Remixed, and has remixed The Plot to Blow Up the Eiffel Tower's song, "INRI," on their INRI ep. Zinner has also remixed Single Frame's song, "People are Germs," in addition to appearing in the music video.

In early 2011 Zinner contributed guitar to the song "Go" by Santigold.

In May 2011 Zinner was commissioned to curate, compose and lead a performance 41 Strings in NYC to celebrate the 41st Earth Day. The performance, in which he collaborated with musicians Hisham Bharoocha and Ben Vida, involved 41 players of various stringed instruments, plus additional percussion and synthesiser parts.