Soon after the graduation Robert Atayan started his research in the field of Armenian folk and medieval music. He studied Khaz music notation system (based on ancient neumes) and started teaching at the Yerevan Conservatory in 1944. Atayan became an assistant professor in 1955 and head of the Music Theory & Composition department in 1962. He was also a senior researcher at the Art Institute of the Armenian NAS since 1956.
Atayan was a chief editor and compiler of the unabridged Academic Edition of Komitas Works in 8 volumes, printed in Yerevan in 1960–98. He organized various expeditions to research folk music and had been participating in the international conferences in Armenia, Russia, Poland, Germany, England, France, and the USA. As a composer, Robert Atayan wrote a number of chamber instrumental and vocal pieces, often inspired by Gusans music and medieval melodies.