Gold-iron binary alloy nanoparticles delivering next to magneto-plasmonic properties, surface available for the bio-conjugation. The combination of noble and less expensive metal such as nickel, iron or cobalt, is a widespread tool for a biomedical application like MRI/optical-dual imaging or photothermal therapy. For this purpose, the laser-generated nanoparticle is advantageous due to control over the atomic composition and alloying degree. Nevertheless, properties of such nanomaterials are morphology dependent. Hence, synthesis of various structures such as alloy, Core-Shell, multi core-shell is possible, yet the design over the ultrastructure is still challenging, due to a lack of a fundamental understanding of the synthesis process. A recent intensively studied concept is a mechanistic model, created based on the combination of experimental and theoretical approaches. In this study, the nanoscale phase diagram for binary AuFe alloy system synthesized via laser ablation was designed based on a combination of experimental data and the thermodynamic calculations. In this regard, various nanoparticle compositions were considered. In the second part, an experimental approach was used, due to the lack of a theoretical model considering the complexity of the liquid environment and kinetically controlled processes. In this regard, the influence of laser parameters, such as target composition, liquid environment and pulse duration on the final ultrastructure was investigated. In this context, ideal conditions regarding the synthesis of iron-gold Core-Shell nanoparticles were determined. At last based on data gathered from the experimental approach combined with thermodynamic calculations, a mechanistic model for nanoparticle formation mechanism was summarized. Finally, proposed models’ transferability was successfully confirmed by another magneto-plasmonic binary system, in this case, AuCo.