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Molecular beam deposition was employed to synthesize Ag–Pt bimetallic nanoparticles, particularly Janus nanoparticles, embedded within photopolymer films under controlled conditions. This approach fills a key literature gap, as previous studies have focused on either polymer-based Janus nanoparticles or metallic nanoparticles as separate systems. Precise tuning of deposition mode (co-deposition versus sequential), layer sequence (Ag/Pt or Pt/Ag), and Ag content produces anisotropic architectures with spatially segregated Ag and Pt domains. Phase segregation dominates over alloying or core–shell formation, driven by large differences in cohesive energy, atomic radius, and lattice strain, combined with limited room-temperature atomic mobility. The photopolymer substrate promotes domain separation through tunable surface chemistry and interfacial asymmetry. Rapid deposition kinetically traps Janus morphologies, while extended Ag exposure generates ramified JNPs with increased heterogeneity. Co-deposition produces nearly homogeneous alloys, whereas sequential strategies yield asymmetric particles: Ag/Pt leads to acorn-like Janus structures, while Pt/Ag results in fragmented, patchy alloys. Each configuration shows distinct optical responses, verified by UV–vis spectroscopy. Combined insights from grazing incidence small- and wide-angle X-ray scattering, angle-resolved X-ray photoelectron spectroscopy, and scanning transmission electron microscopy coupled with energy-dispersive X-ray analysis confirm anisotropic phase segregation and structural diversity. Overall, these findings establish MBD on photopolymer substrates as a versatile and broadly applicable platform for the design of anisotropic bimetallic nanostructures with tunable structural, chemical, and optical functionalities.