Abstract The structural changes of an iron molybdate/molybdenum oxide (Mo/Fe=2.0) catalyst for the selective oxidation of methanol to formaldehyde were studied using combined operando X‐ray absorption spectroscopy (XAS) and X‐ray diffraction (XRD) as well as operando Raman spectroscopy. Under operating conditions, the Mo K‐edge XANES spectra showed a transition from a mixture of α‐MoO 3 and Fe 2 (MoO 4 ) 3 towards only Fe 2 (MoO 4 ) 3 . XRD and Raman spectroscopy also showed disappearance of the α‐MoO 3 phase with time on stream. The results evidenced that the α‐MoO 3 component evaporated completely, while the Fe 2 (MoO 4 ) 3 component remained stable. This was linked to a decrease in catalytic activity. Further studies unraveled that the rate of α‐MoO 3 evaporation increased with increasing MeOH concentration, decreasing O 2 concentration and increasing temperature. The simultaneous measurements of catalytic activity and spectroscopy allowed to derive a structure‐activity relationship showing that α‐MoO 3 evaporation needs to be prevented to optimize MoO 3 ‐based catalysts for selective oxidation of methanol.