It was, for the first time, demonstrated by means of FTIR, EXAFS, XPS, and XRF techniques that thermally stable Co–Mo binary sulfide clusters were synthesized in NaY zeolite cavities using Co and Mo carbonyls as precursors. The hydrodesulfurization (HDS) and hydrogenation activities of the intrazeolite nanocomposite sulfide clusters were examined as a function of composition. It was found that the highest HDS activity was attained at Co/Mo ≃ 1 (2 Mo/super cage or 12 wt. % Mo) and that the Co sites of the clusters were responsible for the reactions. The composition of the catalytically active intrazeolite Co–Mo sulfide clusters was implied to be Co2Mo2S6. The present intrazeolite nanostructure approach strongly suggested that the Co–Mo binary sulfide formation played a prominent role in the catalytic synergy generation. Metal carbonyl techniques were used in the preparation of intrazeolite Fe–Mo binary sulfides.