He was appointed professor at the University of Graz in 1972 and was head of the institute of liturgics, Christian art and hymnology until his retirement in 1999.

Inspired by the Second Vatican Council, he contributed to the first common Catholic hymnal in German, Gotteslob, and supported ecumenism especially with Orthodox Churches, as a member of the board of Pro Oriente from 1986.

[1] After years as a chaplain in Arnfels and Hartberg, he became secretary of the bishop of Graz, Josef Schoiswohl [de], in 1959.

[1][5][6] He was appointed professor at the University of Graz in 1972, and served until his retirement in 1999 as head of the institute of liturgics, Christian art and hymnology.

[8] He was awarded an honorary doctorate in Orthodox Theology from the Lucian Blaga University of Sibiu in Romania in 1997.

[1][2][8] In response, Bertl Muetter composed 1+1+1=1 (discursus trinitatis) for three groups of musicians, which premiered in 2011 at the Graz Cathedral and was dedicated to Harnoncourt.

[11] In 2011 he founded, supported by his five siblings, an association to rescue and restore a chapel, the late-Gothic Heiligen-Geist-Kapelle in Bruck an der Mur.

Today, the deadly plagues for the whole earth are the wanton destruction of soil, water and air - gifts that the Creator has entrusted to mankind for preservation.

[a][14] The restored building was inaugurated on 7 June 2020, Trinity Sunday that year,[1][15] Harnoncourt had hoped to have the Chapel completed by that day.