During the '80s, Kaiser projects tended toward the rock sound of the '60s and '70s, with a special fascination for the music of the Grateful Dead and participation in a number of tribute albums for Imaginary Records. Just when people were starting to peg him as a "cover artist," Kaiser ditched his rock stylings, for the most part, and went back to more of a free improvising style. He recorded albums with Derek Bailey and Jim O'Rourke, and did new recordings with his old duo partner Fred Frith. The '90s also saw Kaiser increase his profile through his successful collaborations with David Lindley and local musicians from both Madagascar and Norway. He was also involved with a number of recordings made in Burma, also for the Shanachie label. The late '90s saw another stylistic shift, when Kaiser joined forces with trumpeter Wadada Leo Smith for a tribute to the early-'70s sound of the electric Miles Davis bands. The project lasted for several years with a rotating lineup and produced several releases, including 1998's Yo Miles! on Shanachie and a pair of mid-2000s releases on Cuneiform, Sky Garden and Upriver. In late 2001/early 2002 Henry Kaiser joined a group of scientists for two and a half months in Antarctica, where he became the first musician to record on that continent (some of this music has been released digitally).

Kaiser appears to be constantly busy, recording in different settings, although his release schedule is sometimes not as active as his recording schedule, a case in point being the release in 2003 of Guitar Party with Glenn Phillips, which was actually recorded in 1990. However, Kaiser has remained active in performing and recording with a variety of projects (including and in addition to Yo Miles!) in the 21st century, including an avant improvising power trio with drummer Weasel Walter and drummer Damon Smith (releasing Plane Crash in 2009). Kaiser also collaborated on Richard Thompson’s original score to the 2005 Werner Herzog film Grizzly Man. In addition, Kaiser is a noted underwater photographer, and his photography has in fact served as an inspiration for Herzog’s own film work. Herzog's 2005 sci-fi film The Wild Blue Yonder used some of Kaiser’s footage, and the German director’s 2007 Antarctica documentary Encounters at the End of the World featured more Kaiser underwater photography; Kaiser also produced the latter film and co-composed and performed the music of its original score with David Lindley.