During his studies in Cologne Chisholm developed a system of micro-tonal fingerings for saxophone and so called "split-scales" which he presented on his 1996 debut solo CD Circe on Jazzhaus Musik.

During his studies in Cologne he met many musicians he still collaborates with today including Marcus Schmickler, Nils Wogram, John Taylor, Felix Fan, Adrian Brendel, Burnt Friedman, Jochen Rückert, Antonis Anissegos, Jaki Liebezeit, Claudio Bohorquez.

His work with her is wide-ranging, from composing the music for major site-specific installations "Moonmirror" (Mallorca, 2003), "Lumiere en Prison" (Paris, 2002), Spiriti de Madre Perla" (Naples, 2002), "Twilight Transit" (NYC 2004), Heart Shadows (Lisbon, 2005), "Das Universum in einer Perle" (Berlin, 2006), to recomposing the music for her early performance films which was released on a complete DVD set in 2005.

In 2009 he composed the music for her film Fata Morgana which was premiered at the Teatro La Fenice Opera House during the Venice Biannale.

In 2001 he composed music for the German Theater (Deutsches Schauspielhaus) in Hamburg, working on Maria Stuart by Schiller and Arabische Nacht by Schimmelpfennig.

In 2006 and 2007 he was musical director of the Earth Festival in Kenya which featured a large cast of international musicians, including Huun Huur Tu.

In 2015 Hayden Chisholm contributed to Waywords and Meansigns, a collaborative project setting James Joyce's Finnegans Wake to music.