He eventually attained the named chair of Herbert C. Youtie Distinguished University Professor of Papyrology.
Through Merkelbach, he was introduced to papyrology (the study of ancient papyri, a writing medium preserving classical literature) and the considerable papyrus collection of the University of Cologne.
[1] In 1967 he and Merkelbach founded Zeitschrift für Papyrologie und Epigraphik, the most important journal in papyrology and ancient Mediterranean epigraphy, where he served as an editor.
After research stays in Oxford and London, Koenen completed his habilitation in 1969 at the University of Cologne.
[4][1] Koenen's most significant work may have been his research and publications on the Cologne Mani-Codex, a document containing more information on Manichaeism and the obscure Elchasaites, a Jewish Christian sect in Babylonia.
The couple had three sons and a daughter together, including the Old Testament scholar Klaus Koenen [de].