Along with fellow Boston experimental musician Robin Amos, Jones formed Cul de Sac in 1990. The two would be the only constant members throughout the band's lifespan. Over the next two decades, the band would release a plethora of albums, singles, and EPs, focusing almost entirely on instrumental pieces and developing a signature sound melding noisy electronics, finger-style acoustic guitar, and terse rock rhythms. Jones occasionally played homemade instruments of his own design on these recordings, including a prepared lapsteel guitar he dubbed “the Contraption.”

A self-proclaimed student of what he calls "the Takoma School,” Jones' instrumental style heavily follows the influence of John Fahey and falls generally into the rustic pastoral territory of Fahey and other American Primitive artists. In 1997, Jones collaborated with Fahey on The Epiphany of Glenn Jones, a rough-hewn pastiche of sound collage, collective jamming, and several spoken word pieces. In the early 2000s, Cul de Sac's activity slowed down significantly, and Jones began work on solo recordings. These discs moved away from Cul de Sac's ever-shifting but usually loud sonics toward a more stripped-down, gentle approach. This Is the Wind That Blows It Out was released by Strange Attractors Audio House in 2004; Jones would issue two other solo discs with Strange Attractors Audio House, including Against Which the Sea Continually Beats in 2007 and Barbecue Bob in Fishtown in 2009, which included his first forays into banjo playing.

In 2011, Jones released The Wanting, his first album with Chicago post-rock flagship label Thrill Jockey. The Wanting more deeply explored open tunings and featured “The Orca Grande Cement Factory at Victorville,” an extended duet with powerhouse percussion improviser Chris Corsano. He followed in 2013 with My Garden State, an album written in Jones' boyhood New Jersey home while he was caring for his ailing mother. Welcomed Wherever I Go, an EP featuring a collaboration with Cian Nugent, appeared in 2014. Full-length Fleeting, recorded in a creekside house in Mount Holly, New Jersey, was issued by Thrill Jockey in 2016. ~ Fred Thomas