We have carried out detailed microstructural studies of phase separation and grain boundary composition in Cu2ZnSnS4 based solar cells. The absorber layer was fabricated by thermal evaporation followed by post high temperature annealing on hot plate. We show that inter-reactions between the bottom molybdenum and the Cu2ZnSnS4, besides triggering the formation of interfacial MoSx, results in the out-diffusion of Cu from the Cu2ZnSnS4 layer. Phase separation of Cu2ZnSnS4 into ZnS and a Cu–Sn–S compound is observed at the molybdenum-Cu2ZnSnS4 interface, perhaps as a result of the compositional out-diffusion. Additionally, grain boundaries within the thermally evaporated absorber layer are found to be either Cu-rich or at the expected bulk composition. Such interfacial compound formation and grain boundary chemistry likely contributes to the lower than expected open circuit voltages observed for the Cu2ZnSnS4 devices.