He found his true voice as an electro-acoustic improviser via a series of duets, trios and quartets beyond the conventions of (classical, jazz, rock) traditions, blending naturally into the soundscapes created by his collaborators: Christian Marclay on Live Improvisations (june 1993 - For Four Ears, 1994); Jim O'Rourke on Slow Motion (may 1994 - For 4 Ears, 1995) and Weighting (july 1997 - For 4 Ears, 1998); Masahiko Okura, Taku Sugimoto, and Otomo Yoshihide on Metal Tastes like Orange (Amoebic, 1999); Voice Crack on Table Chair And Hatstand (march 1996 - For 4 Ears, 1996), Poire_z (march 1999) also featuring Erik M on turntables, and Buda_rom (october 2000 - For 4 Ears, 2000); Otomo Yoshihide and M. Sachiko on Filament 2 (july 1998 - For 4 Ears, 1999) and Filament 3 (For 4 Ears, 2000); Keith Rowe and Taku Sugimoto on The World Turned Upside Down (Erstwhile, 2000); Taku Sugimoto on I Am Happy If You Are Happy (october 1999 - For 4 Ears, 2000); percussionist Le Quan Ninh on La Voyelle Liquide (january 2000 - Erstwhile, 2000); Oren Ambarchi and Voice Crack on Oystered (july 2002 - Audiosphere, 2003); guitarists Oren Ambarchi and Philip Samartzis on Strange Love (october 2003 - For Ears, 2003); Otomo Yoshihide on Time Travel (october 2002 - Erstwhile, 2003); with Nmperign (trumpeter Greg Kelley and saxophonist Bohb Rainey) on More Gloom More Light (august 2002 - Rossbin, 2003); with guitarist Tomas Kober and laptop musician Steinbruechel on Momentan Def (november 2002 - Cut, 2003); with the ARTE Quartet and saxophonist Urs Leimgruber on E_a.sonata.02 (november 2002 - For Eats, 2004); etc. Some of these are only "virtual" collaborations: Mueller assembles the compositions in his studio by manipulating the original sources submitted by the other musicians.

Eight Landscapes (june 2002 - For4ears, 2003) is (finally) a solo work. Each landscape indulges in a different kind of "noise", and thus the album as a whole stands as an artistic manifesto of sorts.

Points And Slashes (april 2004 - Erstwhile) documents a 2004 studio jam between Muller on digital soundscapes and Japanese guitarist Tetuzi Akiyama on manipulated guitar. Muller basically replaced the percussions of his beginnings with digitally sculpted "glitchy" percussive sounds.

Wild Suzuki (2006) documents a live improvisation with Moslang (Voice Crack). Tanker (april 2004) was a long-distance collaboration with saxophonist MAsahiko Okura and vocalist Ami Yoshida.

Other collaborations: Shift (september 1997) with Hans Burgener on violin and Richard Teitelbaum on electronics; Metal Tastes Like Orange (july 1998) with Masahiko Okura on alto sax, Otomo Yoshihide on turntables, Taku Sugimoto on guitar; 11 Ways To Proceed (november 1998) with Hans Burgener on acoustic and electric violin; Richard Teitelbaum on electronics, Carlos Zingaro on violin; Streaming (april 2001) with Dieb 13 on turntables and Jason Kahn on percussion and electronics; Presque_Chic (april 2000), credited to Poire_z (Erik M on turntables and Voice Crack); + (may 2001), credited to Poire_z (Erikm on sampler, Voice Crack, Sachiko M on sinewaves, Christian Marclay and Otomo Yoshihide on turntables); Boom Box (october 2001) with Norbert Moeslang (half of Voice Crack); Q (may 2002), again credited to Poire_z (Erik M on "3k_pad.system", Voice Crack and vocalist Phil Minton); Wireless Within (july 2002) with Philip Samartzis on electronics and Voice Crack on "cracked everyday-electronics"; Tint (october 2002) with Toshimaru Nakamura on "no-input mixing board"; Intersecting a Cone with a Plane (march 2003) with Ricardo Arias on "bass-balloon kit" and Hans Tammen on "endangered guitar"; Why Not Bechamel (may 2003) with Erikm on "3k.pad-system" and Toshimaru Nakamura on "no-input mixing board"; Blinks (may 2003) with Jason Kahn on powerbook; Skyshifter (july 2003) with guitarist Mark O'Leary; Wild Suzuki (april 2004) with Norbert Moeslang on "cracked everyday-electronics"; Drumming (october 2004) with Jason Kahn on laptop and Christian Wolfarth on percussion and Mller only on ipod and electronics; Perspectives (november 2004) with Steinbruchel on laptop; Fibre (november 2004) with guitarists Tomas Korber and Keith Rowe; Yamaguchi (march 2006) with the Signal Quintet (Jason Kahn on synthesizer, Tomas Korber on guitar, Norbert Moeslang on electronics, Christian Weber on contrabass); etc.

The solo Reframed (2005)

The double-CD Live & Replayed (june 2006) documents three live jams for iPod and electronics and three computer remixes of the same jams.

Skyshifter (july 2003) is a collaboration with Mark O'Leary (guitar, electronics, implements, ebow, samples).

The trio of Jason Kahn (analog synthesizer), Günter Müller (electronics), and Christian Wolfarth (percussion) is documented on Drumming (Creative Sources, 2005) and Limmat (march 2009).

The double-CD Buenos Aires Tapes (Monotype, 2011), recorded in february 2006, documented a quintet with Alan Courtis (unstringed guitar, tapes), Pablo Reche (sampler, mds, electronics), Sergio Merce (4-track portastudio without tape, WX7) and Gabriel Paiuk (piano, tape).

Cym_bowl (Mikroton, 2011), recorded in 2007-08, presents solo music for cymbals, singing bowl and processing.

The Afternoon Saints of Shirley Jangle (K-Raa-K, 2010) were turntablist Christian Marclay, Swiss percussionist Gunter Muller, Sonic Youth's guitarist Lee Ranaldo and bagpipe player David Watson.

Ground (september 2017) documents a live collaboration with Kurt Liedwart (electronics) and Norbert Moslang (cracked everyday electronics).

The quintet of Gunter Muller (ipods, electronics), Jason Kahn (modular synthesizer, radio, mixer), Norbert Moslang (electronics), Joke Lanz (turntables) and Christian Weber (bass) recorded the lengthy Kangaroo Kitchen and Mountain Monkey on the double-disc Kangaro Kitchen (september 2018).

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