The elucidation of structure‐activity correlations in selective oxidation of propylene and isobutene over mixed metal oxides (MMO) is attractive for knowledge‐based catalyst design and process optimisation. Particularly, 4‐component Bi‐Mo‐Co‐Fe‐O catalysts need to be studied since their complex metal oxide phase mixture leads to higher activity and selectivity than 2‐component Bi‐Mo‐O. Hence, three Bi‐Mo‐Co‐Fe‐oxides with different metal ratios were prepared by hydrothermal synthesis and compared during selective oxidation tests with propylene and isobutene. The active phases after several days on stream were investigated by synchrotron X‐ray diffraction (XRD) and Raman spectroscopy, while the structural evolution under reaction conditions was followed by operando Raman spectroscopy, synchrotron XRD, and multi‐edge X‐ray absorption spectroscopy. Similar structural transformations were observed during selective oxidation of propylene and isobutene, with similar influence on catalytic performance. A phase mixture of β‐CoMoO4/β‐Co0.7Fe0.3MoO4, γ‑Bi2MoO6, Fe3O4 and Bi3FeMo2O12 was observed, whereby high amounts of β‑CoMoO4/β‐Co0.7Fe0.3MoO4 increased selectivity to acrolein/ methacrolein. In contrast, high amounts of γ‐Bi2MoO6 and Fe3O4 favoured total oxidation to CO and CO2. The simultaneous presence of β‐CoMoO4/β‐Co0.7Fe0.3MoO4, Bi3FeMo2O12 and Fe2O3 increased selectivity to methacrolein in isobutene oxidation, whereas no comparative increase in acrolein selectivity was observed in propylene oxidation. This suggests different key active phases in both reactions.