Apo alpha-lactalbumin (apo alpha-LA) and lysozyme (LYS), two homologous globular proteins have been shown to be able to interact and self-assemble to form microspheres. We report on the organisation and the mechanism of such protein assembly process using a variety of microscopic techniques. We demonstrated that proteins involved into apo alpha-LA/LYS microspheres exchange with those free in solution. The exchange process takes place from the periphery to the centre of the microspheres. The formed spherical particles observed after fixed incubation time were found to be either individual or aggregated according to the total protein concentration leading to structures with different size and morphology. It appears that protein assembly occurs throughout successive steps of aggregated spherical particles that reorganise into biggest isolated microspheres. Direct microscopic observations over time confirm that microspheres resulted from a reorganisation of aggregated, clustered nanospheres. We propose that the formation of apo alpha-LA/LYS microspheres follows an "aggregation-reorganisation" mechanism.