A few dozen people filed into the Wetlands Preserve on September 2nd, 1990, to see the lead singer of Blues Traveler sit down with just an acoustic guitar, a capo and a microphone to play a set of unplugged tunes that did not figure into the regular Blues Traveler repertoire. As he began his set he excused himself by saying "I've never done this before, so go easy on me if I screw up." Over two sets lasting nearly two and a half hours, John played over twenty songs that had never been heard before on stage, and the first Blues Traveler side project was born.

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.