Austenitic stainless steel D9 is a candidate for Generation IV nuclear reactor structural materials due to its enhanced irradiation tolerance and high-temperature creep strength compared to conventional 300-series stainless steels. But, like other austenitic steels, D9 is susceptible to irradiation-induced clustering of Ni and Si, the mechanism for which is not well understood. This study utilizes atom probe tomography (APT) to characterize the chemistry and morphology of Ni–Si nanoclusters in D9 following neutron or proton irradiation to doses ranging from 5–9 displacements per atom (dpa) and temperatures ranging from 430–683 °C. Nanoclusters form only after neutron irradiation and exhibit classical coarsening with increasing dose and temperature. The nanoclusters have Ni3Si stoichiometry in a Ni core–Si shell structure. This core–shell structure provides insight into a potentially unique nucleation and growth mechanism—nanocluster cores may nucleate through local, spinodal-like compositional fluctuations in Ni, with subsequent growth driven by rapid Si diffusion. This study underscores how APT can shed light on an unusual irradiation-induced nanocluster nucleation mechanism active in the ubiquitous class of austenitic stainless steels.