Despite weak health, which for many years permitted him to leave his room only at rare intervals, he worked on until his death in Baden, near Vienna.
While in Heliligenkreuz, Janauschek composed his first major work, Originum Cisterciensium Liber Primus (Vienna, 1877), in which he describes the foundation of the Cistercian Order, its organization and extension, and mentions many of those who, under various titles, had honoured it.
He was unable to publish the second volume, which was to have been devoted to Cistercian nunneries, and for which he had collected a great deal of material.
In 1891, on the occasion of the eighth centenary of the birth of Saint Bernard of Clairvaux, the Cistercian Congregation of Austria prepared four volumes, under the title of Xenia Bernardina.
Janauschek gave assistance in the preparation of the first three volumes, but the fourth, Bibliographia Bernardina (Vienna, 1891), was entirely his own work.