Born to German parents in the Russian city of St. Petersburg, Beilstein studied chemistry in Germany under Bunsen, Liebig, and Wurtz and gained his PhD under Wöhler at Göttingen (1858). He was lecturer at Göttingen (1860–66) and from 1866 professor of chemistry at the Technological Institute at St. Petersburg.

Beilstein's many researches in organic chemistry included work on isomeric benzene derivatives. He is better remembered, however, for his monumental Handbuch der organischen Chemie (1880–82; Handbook of Organic Chemistry), in which he set out to record systematically all that was known of every organic compound. He produced the second (1886) and third (1900) editions, after which the work was assigned to the Deutsch Chemische Gesellschaft, who have published it ever since.