With the advent of high-brilliance synchrotron sources, the issue of beam damage on the samples deserves proper attention. It is especially true for operando studies in batteries, since the intense photon fluxes are commonly used to probe ever finer effects. Here we report on the causes and consequences of synchrotron X-ray beam damage in batteries, based on the case study of operando X-ray diffraction. We show that beam damage is caused by the mingled actions of dose and dose rate. The aftereffects can lie in a broad range, from mild modifications of the crystalline structure to artificial phase transitions, and can thus impede or bias the understanding of the mechanisms at play. We estimate the doses at which the different effects appear in two materials, suggesting that it could be expanded to other materials with the same technology. We also provide recommendations for the design of operando synchrotron experiments.