Co–Ag nanocrystalline films deposited by Pulsed Laser Deposition were irradiated by excimer laser at different values of energy fluence. The microstructural modifications induced by such treatment were investigated (by atomic force, scanning and transmission electron microscopies) and correlated with the magnetic and magnetotransport properties. The results indicate that laser irradiation favors the silver grain growth and induces a segregation of a fraction of Co, driven by the interface energy, to sites energetically more favorable like Ag grain boundaries (as small grains with diameters less than 5 nm, to be compared to ≈10 nm in the as-deposited sample) and the film/substrate interface. Such microstructural variation leads to changes in the magnetic behavior and to an increase of the magnetoresistance below 10 kOe.