Magle has gained a reputation as an organ virtuoso,[1][2][3] and as a composer and performing artist who does not refrain from venturing into more experimental projects – often with improvisation – bordering jazz, electronica, and other non-classical genres.

Later, Znaider gave the first performance of Magle's variations for violin and piano in the Concertgebouw, Amsterdam, with the pianist Daniel Gortler: Journey in time describes a "kind of scenes or musical images" with the use of sharp dissonances, complicated rhythms and dramatic transitions and thematic formations.

Other artists involved were the architect Thomas Wiesner, sculptors Anders Krüger and Frans Jacobi, painter Tomas Lahoda, and the costume designer Annette Meyer; it was presented as a contemporary "Gesamtkunstwerk" comprising architecture, art, music, and performance.

That goes for the often occurring contrast between very bright and very dark timbres, between clearly defined melodic lines and closely woven fields of sound, between huge pillars of chords and energetically moving patterns of rhythm.

And it goes for his two dominating ways of structuring his music as well (...) the gradual building of dynamic tensions through adding more and more layers of sound, the abrupt changes between light and dark, force and calm, clear and veiled.

Including the courage to extend some of the parameters into the extremes – such as when a rhythmic pattern becomes so dense as to almost blurring the contours of the figurations involved, and only the outline of movement remains...The Christmas cantata A newborn child, before eternity, God!

[20] The work sets text from a kontakion by the 6th century hymnographer Romanos the Melodist, translated into Danish by the theology professor Christian Thodberg, and edited by the priest Kristian Høeg.

It was premiered on 24 August 1997 at a concert in St George's Chapel, Windsor Castle by the London Philharmonic Orchestra conducted by David Parry, with Magle himself on piano.

The cantata's text is by the author Iben Krogsdal; based on the story of Saint Cecilia, who died in a gruesome way for her Christian faith, it has been described as "moderate modernism" with a special "Danish tone" and a transparent chamber musical instrumentation.

Magle premiered the work, his Rhapsody for organ Viva Voce, at two gala concerts on 12–14 May 2009 in Aarhus Cathedral and Vangede church, in collaboration with Dame Gillian Weir.

Magle created its specifications and tonal design, after the old organ had perished in a fire five years earlier while in storage; he gave the instrument's inauguration concert on 8 November.

[33] The organist, jazz-pianist, and composer Henrik Sørensen defended Magle's free improvisational form in an article in Danish organ-magazine Orgelforum.

[3] Magle composed the work Fanfare and Anthem 'Skyward' for brass ensemble, timpani and percussion which was premiered at the rollout ceremony for the Danish F-35 fighter jets on April 7, 2021.

[38] Lys på din vej was released on an album with the same title the following year, which received mixed reviews, being criticized especially by the newspaper Politiken for consisting of "endless repetitions of the same melodic material without development".

The fanfare was originally planned to be premiered at a gala concert at the Royal Danish Theatre's Old Stage, but due to the corona-lockdown the music was instead recorded by the musicians individually in their own homes and subsequently edited and presented to the queen[46] On June 7 the same year the fanfare received its live premiere, conducted by Thomas Søndergaard at the re-opening of the Royal Danish Theatre.

[48] Magle's first CD, Sangen er et eventyr – Sange over H.C. Andersens eventyr (The song is a fairytale – Songs based on fairytales by Hans Christian Andersen), of 1994 was recorded with the jazz double bassist Niels-Henning Ørsted Pedersen, the jazz-pianist Niels Lan Doky, the percussionist Alex Riel, Trio Rococo, and vocalist Thomas Eje.

[50] The collaboration received positive reviews in the Danish press, with Jyllands-Posten calling the track "Nyt Pas" from Elektra "glowing orchestral hip hop with mature ambitions",[51] and the music magazine Gaffa describing the contrasts between Frederik Magle's classical compositions and Suspekt's hip hop as "extreme opposites that helped to make the evening special" in their review of the release concert in Koncerthuset, September 2011.