Schaefer's early experiments are documented by cassettes such as Architectural Cleaner Required (AudiOh, 1994), 95 Degree Angles (Audioh, 1995), Disturbed in Disguise (Audioh, 1996).

His albums include music for turntables, recorded on His Master's Voices (Audioh, 1997) and the live OUT (K-RAA-K]3, 1999), Above Buildings (Fat Cat, 2000), an exercise in musique concrete, On/Off LP (Audioh, 2001), Comae (Rhyz, 2001), a collaboration with Robert Hampson, Eccentric/Concentric (AudiOh, 2001).

They focus on two elements: studio manipulation of field recordings, and his self-built twin and triple armed varispeed turntables. The resulting "musique concrete" is unusually dense, "warm" and seductive.

Based upon a novel by J.G. Ballard, Pulled Under (Augioh, 2002) displays Schaefer's skills at mixing his sources to produce clusters and sheets of morphing sounds that often recall the pieces of such classical composers as Penderecki, Ligeti, Part and Stockhausen. But Schaefer explores the inner nature of sound: Penumbral Rover employs "radio signals from the sun recorded during a solar eclipse"; Vertrek borders on silence. Maison A Bordeaux differs from the others in that it has a plot full of twists, and mostly surreal ones, worthy of Becket's absurdist theater. His background as an architect (geometry, space, harmony) is evident in the album's centerpiece, Parallel Spoor, that takes ideas from such disparate schools as LaMonte Young, Pierre Henry and Oval and turns them into an ordered set of events.

Le Petit Theatre De Mercelis (Audiosphere, 2002), a 50-minute piece, was recorded live in Brussels.

Black Immure (SIRR, 2003) documents a live performance based on manipulated field recordings and looped piano patterns.

Skate / Rink (Audion, 2003) is not art, but a joke on making art. The first disc contains music-making tools and the second disc contains 99 brief tracks to be played randomly.

Comae (Rhiz, 2003) is a collaboration with Main's Robert Hampson.

The EP Weather Report (Alluvial, 2003) is the modern equivalent of a Dutch landscape painting of the 16th century: a gloomy portrait of winter via field recordings of sounds associated with weather events.

Quality Hotel (Mutek, 2003) is a collaboration betweem Janek Schaefer, Radboud Mens, Stephan Mathieu, and Timeblind.

Cold Storage (DSP, 2004) is one of Janek Schaefer's most refined works of "musique concrete". The original concert was a live improvisation using as an instrument the snippets he had previously collected and assembled. The CD version uses the same sounds, but "keeps it closer to the source material". Luckily, it is not apparent at all that he kept it so "close" to the original source. The five movements are powerful and haunting precisely because the sources are unrecognizable, and, instead, the slowly evolving music seem to hark back to mysterious primitive forces of nature. The first movement sounds like the internal, psychological perception of the composer entering a room. The second sounds like a broader survey of the environment, evoking a multitude of action, from traffic to waves. Its ebullient chaos is balanced by the ghostly and massive moving textures of the third movement, The fifth movement is the most fearsome, unleashing industrial fury and expressionist tension. The whole is exactly the sum of its parts: a multi-faceted experience that describes a continuum of emotions through the inner ear.

Recorded in Istanbul, Songs For Europe (Asphodel, 2004) is a collaboration with Philip Jeck a milestone of concrete music that builds ambient soundscapes from old Greek and Turkish records (as well as radio broadcasts). The two virtuosi of record manipulation (Jeck inspired Schaefer as a teenager) employ mesmerizing techniques to make sounds appear and disappear. Taxim is a concerto for intergalactic signals, monster distortion and alien drones. Decomposing vynil is the protagonist of Istanbul Drift, its crackling providing the background to a preacher and then becoming "the" voice itself. Several minutes later, a loud conference of manipulated sounds suddenly jumps out of the quasi-silence. Aegean Sea is the wildest collage, running the gamut from banging noises to hysterical chirping to industrial clangor to tolling bells to nebula-like moaning. Kerameikos is nine minutes of relative quiet, like a slowly revolving 360-degree panorama, a piece of pure ambience. The original sources are revealed a bit in Song for Europe and Acropolis Now.

Walking East (2005) is a collaboration between Janek schaefer (who scored the music) and New York photographer Gino Zardo, five years in the making, that documents music ritual of the world. The 21-minute musical score is a collage of human chants, natural sounds, ethnic instruments and conversations.

Migration (2006) documents a soundtrack for a dance event by Noemie Lafrance and is emblematic of Schaefer's surgical collages of manipulated field recordings.

Hidden Name (Cronica, 2006) is a collaboration betweem Janek Schaefer and Stephan Mathieu, that used their improvisation on acoustic instruments, turntables and field recordings as the sources to manipulate in studio and produce ambient watercolors such as the 20-minute Planets.

In The Last Hour (Room, 2006), a piece in four movements premiered in november 2005, leverages the combination of live instrumentation (piano, organ and clarinet) and textures obtained from turntables and electronic devices to create a symphony of darkness that is both lugubrious and romantic.

Vacant Space (2007) was an audio-visual installation.

Alone at Last (2008) contains Boulevard Peripherique and other pieces composed between 1997 and 2007. Boulevard Peripherique begins with a collage of found voices and traffic noise which are then turned into an eerie soundtrack of interstellar travel.

National Portrait (Room40, 2011), originally a site-specific installation, is a "24-hour album containing 1000xMP3's stored on a USB circuit board housed in a tv remote control".

Double Exposure (2011) collects commissioned compositions for installations, theater and compilations. Phoenix & Phaedra Holding Patterns (2011) documents a live composition (premiered in 2009) for portable radios, FM transmitter, 4 corner speaker PA, found sound textures, & Shruti drone box.

Day of the Demons (2012) was a collaboration with Charlemagne Palestine, containing the 20-minute Raga de l'Apres Midi pour Aude, one of the peaks of pathos of his career: bell tolling and didjeridoo-like droning lay the foundations for the transcendent, metaphysical atmosphere needed by the overdubbed nasal singing, which in turn displays more of a psychedelic quality than a religious one.

Lay-by Lullaby (12k, 2014) was a collection of mediocre post-Eno ambient music.

Unfolding Luxury beyond the City of Dreams (2014) contains elegant ambient meditations such as City Of Dreams and White Lights Of Divine Darkness.

The more ambitious Inner Space Memorial in Wonderland (2014) contains two concept pieces, the 21-minute Inner Space Memorial and the 20-minute Wonderland. The former sounds like a symphonic version of the fluttering analogic electronic music of the new-age era, lost in celestial fluctuating nebulae.

Glitter in my Tears (2017) contains 26 brief ambient pieces.

What Light There Is Tells Us Nothing (2018), which contains What Light There Is Tells Us Nothing, built by manipulating Robert Wyatt music.

On Reflection (2022) documents a collaboration with William Basinski.

At the end of 2023 he designed a cryptic conceptual artwork called "Qqquestion".