She discovered and described the Chicago-endemic flowering plant species Thismia americana described in her doctoral thesis in 1913.
The type specimen was found in what was then a wet-mesic sand prairie at 119th Street and Torrence Avenue in what would become the industrial neighborhood of South Deering.
During the first year (1912–13) she also worked as governess to the daughters of the Dean of the College of Liberal Arts, Melvin A. Brannon.
In 1918 she volunteered at the hospital set up by the university for women students during the influenza pandemic, and eventually ran it.
Her Monograph of the Isoetaceae published in 1922,[8] was the major result of this time and remained a standard reference into the twenty-first century.
Pfeiffer then spent the rest of 1923 and part of 1924 on the family farm of a colleague, Zella Colvin, who had also resigned.