Interested in natural history from a young age, Schaerer trained as a teacher and studied theology in Bern.

During his career as a teacher, orphanage director, and pastor, he researched extensively and maintained correspondence with foreign botanists interested in cryptogams.

Schaerer was best known for his multi-volume work Lichenum Helveticorum Spicilegium ("Anthology of Swiss Lichens"), published in 12 parts from 1823 to 1842.

Despite his interests, he thought he had to obey the wishes of his parents and pursue an ecclesiastical career, and he devoted himself to the study of ancient languages and theology.

Because of the vastness of the field, he decided to specialize in the study of lichens, which were abundant in the nearby Alps, and which were relatively little known compared to the plant flora.

Upon his return to Switzerland in 1814, Schaerer became a high school teacher and vice-principal (conrector) in Bern, but he kept up his botanical research as much as his other duties would allow.

During his annual vacations, he would make collecting trips to the Alps, particularly to Bernese Oberland, Valais, Graubünden, and Ticino.

Schaerer researched extensively and maintained correspondence with foreign botanists interested in cryptogams, including Erik Acharius, Olof Swartz, Elias Magnus Fries, and Heinrich Gustav Flörke.

He simultaneously published Lichenes Helvetici exsiccati, a collection of dried herbarium specimens; this exsiccata series he continued working on until his death.

[5][8] In 1836, Schaerer exchanged the post of orphanage administrator in Lauperswil for that of Belp, which brought him closer to Bern and his friends.

For example, in 1841, the already famous paleontologist and glaciologist Louis Agassiz led a group that climbed to the peak of the mountain Jungfrau in the Swiss Bernese Alps – an elevation of 4,158 m (13,642 ft).

Enriched with his new observations, Schaerer began the publication of his Enumeratio Critica Lichenum Europaeorum ("Enumeration of the European lichens"), an illustrated work that depicted the type species of each genus.

[5] His skepticism towards microscopy is understandable considering that the defects of chromatic and spherical aberration were prevalent at the time – flaws that would not be resolved until better lenses were available in the 1830s.

"[note 4][5] In a description of Schaerer's lichen exsiccata at the herbarium at the Montpellier Botanical Garden, Hervé Harant wrote "Segments of sentences in Latin, reminds us that he was one of those many clergymen who were passionate about lichenology".

[12][13] An lithograph image (created by Hubert Meyer [de]) and brief biography of Schaerer appeared in the journal Taxon's Portraits of Botanists series in 1973.

He noted that in general, Schaerer published "many valuable observations on the morphology and reproductive structures of these lichens", but that "with regard to the delimitation of Umbilicaria species, their variation and nomenclature, he appears to have been very confused".