He was ordained a priest of the diocese of Chur on 25 September 1971 and then continued his studies, earning a doctorate in theology in Fribourg.

[citation needed] His tenure proved controversial to some, as he reaffirmed orthodox Catholic doctrine in strong and uncompromising terms.

[4] Huonder then chose to live out his retirement in an institute of the Society of Saint Pius X, with papal authorization, with the intention of living a quiet and prayerful life, celebrating the Tridentine Mass, and working for Sacred Tradition, the revitalization of which he saw as the only means of restoration of the Church.

[6] His funeral Mass on 17 April was celebrated by Bishop Bernard Fellay, and Huonder was buried at the International Seminary of Saint Pius X in Écône next to the tomb of Archbishop Marcel Lefebvre.

[7] Huonder's successor, Bishop Joseph Maria Bonnemain, attended the funeral, but did not take part in the celebration, due to the irregular canonical situation of the SSPX.