Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles are investigated in real time with in situ synchrotron-based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. The combination of metal–support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. At 300 °C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (> 450 °C). The alloy nanoparticles supported on silica and carbon black are homogeneous in volume, but evidence was found of Pd surface enrichment. In sharp contrast, when supported on alumina, the two metals segregated at 300 °C to produce almost pure fcc Cu and Pd phases. Upon further annealing of the mixture on alumina above 600 °C, the two metals interdiffused, forming two distinct disordered alloys of compositions 30% and 90% Pd. The annealing atmosphere also plays a major role in the structural evolution of these bimetallic nanoparticles. The nanoparticles annealed in forming gas are larger than the nanoparticles annealing in helium due to reduction of the surface oxides that promotes coalescence and sintering.