Alloying by grain boundary diffusion-induced grain boundary migration is investigated by secondary neutral mass spectrometry depth profiling in Ag/Au and Ag/Pd nanocrystalline thin film systems. It is shown that the compositions in zones left behind the moving boundaries can be determined by this technique if the process takes place at low temperatures where solely the grain boundary transport is the contributing mechanism and the gain size is less than the half of the grain boundary migration distance. The results in Ag/Au system are in good accordance with the predictions given by the step mechanism of grain boundary migration, i.e., the saturation compositions are higher in the slower component (i.e., in Au or Pd). It is shown that the homogenization process stops after reaching the saturation values and further intermixing can take place only if fresh samples with initial compositions, according to the saturation values, are produced and heat treated at the same temperature. The reversal of the film sequence resulted in the reversal of the inequality of the compositions in the alloyed zones, which is in contrast to the above theoretical model, and explained by possible effects of the stress gradients developed by the diffusion processes itself.