Abbe, who was born in Eisenach (now in Germany), came from poor parents but managed to become a lecturer at the University of Jena, where in 1886 he collaborated with Carl Zeiss, a supplier of optical instruments to the university, to improve the quality of microscope production. Up till then, this had been an empirical art without rigorous theory to aid design. Abbe's contribution was his knowledge of optical theory. He is known for the Abbe sine condition – a necessary condition for the elimination of spherical aberration in an optical system; such a system he described as aplanatic. He also invented the apochromatic lens system (1886), which eliminated both primary and secondary color distortions and the Abbe condenser (1872) – a combination of lenses for converging light onto the specimen in microscopes.

The partnership between Abbe and Zeiss was a productive combination of Zeiss's practical knowledge and Abbe's mathematical and theoretical ability. After Zeiss's death, Abbe became the sole owner of the Zeiss company.