From there he pared down to the quiet, entirely acoustic moods of Shuffletown (1990) before shifting into the country- and folk-influenced territory of Short Man's Room and Kindness of the World. The latter two albums earned him an excellent reputation among fans of alternative rock and country as a superb singer and songwriter. He followed Kindness with the five-song EP Fireman's Wedding a year later. Henry's lyrics are a central focus of his songwriting, but even though he often writes in the first person, his songs are not "personal" in the manner of musicians who are often called singer/songwriters (a genre he doesn't like to be associated with). He's recorded some excellent country covers, but he's equally interested in soul, funk, and rock & roll.

On Trampoline, released in 1996, Henry veered in an edgier, more rhythm-oriented direction. While he still employs acoustic instruments and even a pedal-steel guitar on several songs, Trampoline (much of which Henry recorded at a studio he set up in his garage) is more clearly defined by its drum loops, loud electric guitars, mysterious voices, and curious sonic textures. For this album, Henry recruited guitarist Page Hamilton from the band Helmet and drummer Carla Azar from the band Edna Swap.

Fuse -- mixed with the aid of Daniel Lanois and T-Bone Burnett -- followed in 1999. Two years later, Henry returned with the enigmatic stunner Scar. This particular release marked his last with Mammoth. He opted for a deal with Epitaph's Anti and entered the studio in December 2002 to record his ninth album, Tiny Voices, his most intricate album to date. A second album on Anti, Civilians, followed in 2007, while a third from the label, Blood from Stars, appeared at the end of the summer in 2009. Henry was wildly busy as a producer for the next two years, helming projects from Allen Toussaint, Salif Keita, Carolina Chocolate Drops, Ramblin' Jack Elliott, Mose Allison, Hugh Laurie, Over the Rhine, Lisa Hannigan, and Me'Shell Ndegéocello, as well as participating in others. He finally got around to recording again in 2011, with his most eclectic collection of songs -- all recorded acoustically -- entitled Reverie, which was released on Anti in October of 2011.