Multi-metallic nanoparticles constitute a new class of materials offering the opportunity to tune the properties via the composition, atomic ordering and size. In particular, supported bimetallic nanoparticles have generated intense interest in catalysis and electrocatalysis. However, traditional synthesis methods often lack precise control, yielding a mixture of monometallic and bimetallic particles with various compositions. Here we report a general strategy for synthesizing supported bimetallic nanoparticles by atomic layer deposition, where monometallic nanoparticle formation is avoided by selectively growing the secondary metal on the primary metal nanoparticle but not on the support; meanwhile, the size, composition and structure of the bimetallic nanoparticles are precisely controlled by tailoring the precursor pulse sequence. Such exquisite control is clearly demonstrated through in situ Fourier transform infrared spectroscopy of CO chemisorption by mapping the gradual atomic-scale evolution in the surface composition, and further confirmed using aberration-corrected scanning transmission electron microscopy.