Manufacturing multifunctional nanocomposite materials and engineered surface nanopatterns involves a strategic blend of topography, crystal structures, and chemistry. Here, we report the controllable formation of crystalline nanoparticles and intermetallic compounds on thin films of metallic glasses (Zr 50 Cu 50 , Ti 50 Cu 50 , and Zr 67 Ag 33 ) irradiated by ultrafast laser beams. Mapping the structural modification of the photoexcited and subsequently heated alloys reveals previously neglected chemical reactions with air, offering a direct solution for incorporating nanoparticles into an amorphous oxide matrix and broadening the range of laser-induced surface self-organization features. Our findings are attributed to the occurrence and enrichment of oxygen surface contamination that reacts with selected elements of the metallic glasses. Additionally, the growth of the crystalline phase from undercooled liquid may originate from the dissolution of oxides. Finally, our results establish that the combination of crystalline nanoparticles on amorphous periodic patterns can be universally obtained in a wide range of binary systems of irradiated metallic glasses.