Binary metallic (Au-Co and Ag-Fe) nanoparticles (NPs) with distinctively different heterostructures at the single-particle level was prepared directly in the gas phase through phase separation and surface segregation. An integrated nanocluster deposition system equipped with a nanocluster source was used to synthesize the heterostructured NPs. A magnetron sputtering gun was used to generate the atomic vapor from Co-Au and Fe-Ag composite targets. During synthesis, the pressure in the nanocluster source was increased to 20-100 Pa by introducing an Ar gas flow. The morphology and structure of the NPs were investigated using TEM and HRTEM. EDS data and composition line scans were obtained using a scanning TEM. A magnetic property measurement system, integrated with a SQUID detection system was used to carry out the room temperature and low-temperature magnetic measurements. It was revealed that under certain synthesis conditions, the growth process of NPs stops within 1-2 cm from the target surface.