Operando X-ray studies of chemical reactions have gained increasing interest lately, fueled by the emergence of a new generation of powerful focused X-ray sources. Although it is well known that ionizing radiation causes damage to samples via radical chemistry, this effect is often overlooked in studies of working devices or catalysts where intense focused beams are used as nanoscale probes. Here, we show how an X-ray nanobeam directly causes a phase transition in shape-controlled Pd nanoparticles and that a large oxidative potential must be applied to counteract the effect. In addition, we present a chemical reaction−diffusion model that offers a plausible qualitative explanation of the observations, and which also suggests that prohibitive concentrations of reactive species will arise under any focused X-ray probe, calling into question the validity of these methods as applied to aqueous chemical and catalytic systems.