Cohn, who was born in Breslau (now Wrocław in Poland), was an extremely intelligent child and progressed through school rapidly, being admitted to the philosophy department at Breslau University at the early age of 14. He later developed an interest in botany but was prevented from graduating at Breslau by the university's anti-Semitic regulations. He therefore moved to Berlin, where he received his doctorate in botany in 1847.

Cohn returned to Breslau, becoming professor of botany there in 1872. He had long argued that the state should be responsible for the establishment of botanical research institutes, and as a result of his campaign the world's first institute for plant physiology was set up in Breslau in 1866. Cohn was director of this institute until his death and in 1870 he founded the journal Beiträge zur Biologie der Pflanzen, mainly for the purpose of publishing work carried out at Breslau.

Cohn's early research concentrated on the morphology and life histories of the microscopic algae and fungi, which led to his demonstration that the protoplasm of plant and animal cells is essentially similar. Later, stimulated by the work of Louis Pasteur, he became increasingly interested in bacteria. His classic treatise Untersuchungen über Bacterien (Researches on Bacteria), published in his journal in 1872, laid the foundations of modern bacteriology. In it he defined bacteria, used the constancy of their external form to divide them into four groups, and described six genera under these groups. This widely accepted classification was the first systematic attempt to classify bacteria and its fundamental divisions are still used in today's nomenclature.

Although Cohn did not believe in the theory of spontaneous generation he was aware that bacteria could develop in boiled infusions kept in sealed containers. He postulated the existence of a resistant developmental stage and through careful observation was able to demonstrate the formation of heat-resistant spores by Bacillus subtilis.

Through his book Die Pflanze (1872) and the printing of many of his popular lectures, Cohn presented the study of biology to a wide and appreciative public. He was also responsible for the publication of Robert Koch's important work on the life cycle of the anthrax bacillus.