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Computer simulations were performed to study the different structures showed by bimetallic nanoparticles synthesized in microemulsions. The fact that a nucleus evolves to a particle by accumulating new layers implies that the sequence of deposition of the metals determines the final structure. As a result, if one of the metals precipitates before the other, the nanoparticle core is formed by the first metal, and the other metal forms the surrounding shell. The resulting segregation of the metals can be caused not only by a difference in the reduction rates of the metals but also by a difference in the nucleation rates. In agreement with experimental results, we demonstrate that the metal segregation resulting from the different critical nucleus sizes of both metals can be minimized by increasing local concentration inside a droplet. This can be reached simply by using higher concentrations and/or favoring a faster intermicellar exchange, that is, using surfactants with higher flexibility. These results are very promising for the design of the best synthetic conditions to obtain a specific nanoparticle structure.