Bimetallic nanoparticles have been extensively studied as electrocatalysts due to their superior catalytic activity and selectivity compared to their monometallic counterparts. The properties of bimetallic materials depend on the ordering of the metals in the structure, and to tailor-make materials for specific applications, it is important to be able to control the atomic structure of the materials during synthesis. Here, we study the formation of bimetallic palladium indium nanoparticles to understand how the synthesis parameters and additives used influence the atomic structure of the obtained product. Specifically, we investigate a colloidal synthesis, where oleylamine was used as the main solvent while the effect of two surfactants, oleic acid (OA) and trioctylphosphine (TOP) was studied. We found that without TOP included in the synthesis, a Pd-rich intermetallic phase with the Pd₃In structure initially formed, which transformed into large NPs of the CsCl-structured PdIn phase. When TOP was included, the syntheses yielded both In₂O₃ and Pd₃In. In situ X-ray total scattering with Pair Distribution Function analysis was used to study the formation process of PdIn bimetallic NPs. Our results highlight how seemingly subtle changes to material synthesis methods can have a large influence on the product atomic structure.