In 1897, the Vienna Secession was formed by artists who had left the Association of Austrian Artists. Between 1898 and 1904, Auchentaller showed his work in 10 Secessionist shows. Auchentaller designed the poster and the catalog covers for the Seventh (1900) and Fourteenth (1902) exhibitions. In 1905, he left the Secession along with Gustav Klimt due to differences of artistic opinion.
Auchentaller was a contributor to the magazine Ver Sacrum, a Secessionist publication, and sat on its editorial board between 1900 and 1901. For this magazine, he contributed two title pages and many graphics. His work consisted primarily of floral motifs and linear drawings influenced by Japanese woodcuts which were the popular during that time. The eighth issue of Ver Sacrum was entirely devoted to Auchentaller.