Plasmonic nanojunctions, consisting of adjacent metal structures with nanometre gaps, can support localised plasmon resonances that boost light matter interactions and concentrate electromagnetic fields at the nanoscale. In this regime, the optical response of the system is governed by poorly understood dynamical phenomena at the frontier between the bulk, molecular and atomic scales. Here, we report ubiquitous spectral fluctuations in the intrinsic light emission from photo-excited gold nanojunctions, which we attribute to the light-induced formation of domain boundaries and quantum-confined emitters inside the noble metal. Our data suggest that photoexcited carriers and gold adatom - molecule interactions play key roles in triggering luminescence blinking. Surprisingly, this internal restructuring of the metal has no measurable impact on the Raman signal and scattering spectrum of the plasmonic cavity. Our findings demonstrate that metal luminescence offers a valuable proxy to investigate atomic fluctuations in plasmonic cavities, complementary to other optical and electrical techniques.