Over the early 1990's, John would play a half-dozen more solo sets, all but one at the Wetlands Preserve, and would also occasionally play a song or two solo at the band's full shows to give the rest of the band a break. As time went by, several of John's solo compositions became part of Blues Traveler's repertoire, including the famous Run-Around, which originated in John's only solo appearance in 1993, on June 24th. By this time Blues Traveler had built up a following and had diverted more of their attention to achieving commercial success, and so John's solo gigs lay dormant for several years until September of 1997, when word got out that he would be opening for a friend at New York's Sidewalk Cafe. John played solo for an hour, and then recruited Eric Schenkman out of the audience to join him on a few new Blues Traveler tunes and some old blues standards. A song that had long since been abandoned by Blues Traveler made a reappearance and the first rumors of a solo project began to surface.

It was not until the summer of 1998 that word got around about John doing some songwriting with Jonny Lang, and in the fall of that same year, John revealed that the band would be taking most of 1999 off and that he had been writing some material for a solo project. John ended up in Hoboken, NJ's Water Music studios with old Cycomotogoat friends Crugie Riccio, Rob Clores and Dave Ares, and drummer Carter Beauford, best known for his work behind the kit of Dave Matthews Band. They ended up releasing the disc known as Zygote in September of 1999 and with "Miserable Bastard" hitting the airwaves earlier in the summer, John's solo career had come full circle as the John Popper Band toured the country for the first time in the fall and winter of 1999, with erstwhile God Street Wine drummer Aubrey Dayle filling in for Carter Beauford on the road.

In late 2003, the band took the fall off so that Chan could prepare for the arrival of his second child, but John felt the itch to work on yet another project. Thanks to front-of-house engineer Bo Mahoney, Popper hooked up with bassist Rob Wasserman, best known for his work with Grateful Dead guitarist Bob Weir in the Dead side project known as Ratdog. The two got together for a show in San Francisco that December, and turntablist DJ Logic, who happened to be in town at the time, dropped in for the whole set. One thing led to another, and in early 2004, John and Logic inaugurated the latest incarnation, dubbed the John Popper Project. JPP features John on vocals and harmonica, DJ Logic, Tad Kinchla on bass and Mosaic drummer Marcus Bleecker on the skins. The band toured during breaks in the Blues Traveler schedule in 2004 and 2005, and their first album was released in September of 2006.

For John's most recent project, he turned to perhaps his oldest friend, longtime New York bar scene stalwart Jono Manson. John and Jono had toured together briefly as part of High Plains Drifter, as well as a string of shows in Italy in the spring of 2003. But other than Jono's guest spot on "Brother John" - and John returning the favor on a few tunes on Jono Manson Band's "Almost Home", the two had never sat down to write and record together. That all changed in 2009, when the two of them struck out on a two-week tour of Italy, followed by a writing session at Jono's Chupadero, NM studio with Shurman lead singer and guitarist Aaron Beavers. The result was a band called John Popper & the Duskray Troubadours, and their self-titled release came out in early 2011, followed by a monthlong tour.