Multimetallic nanoparticles possess a variety of beneficial properties with potential relevance for various applications. These metallic nanoparticles can consist of randomly ordered alloys, which retain the properties of the constituting elements, or ordered intermetallics, which possess extended properties. Depending on the desired application, specific alloys or intermetallic compounds are required. However, it remains challenging to achieve particular morphologies, crystal structures, chemical compositions, and particle sizes because of the inherent complexity of nanoparticle synthesis. In this work, Au-Sn nanoparticles were synthesized using a continuous one-step gas-phase synthesis method that offers the possibility to anneal the nanoparticles in flight directly after generation to tune their properties. The bimetallic model system Au-Sn, comprising both alloys and intermetallic compounds, was studied in the temperature range of 300 to 1100 °C. The bimetallic Au/Sn ratio in the nanoparticles can be adjusted with in-flight annealing between 70/30 and 40/60 atomic %. While Au-rich alloys are obtained at lower temperatures, the increase in the annealing temperature leads to the formation of more Sn-rich intermetallic phases. Surface and size effects greatly influence particle morphologies and phase fractions. This research opens new opportunities for the synthesis of customized nanoparticles by temperature adjustment and particle size selection.