We report the phase and size-controlled synthesis of Fe-Pt nanoalloys, prepared via a two-step synthesis procedure. The first step is the deposition of bilayers consisting of iron oxide and Pt films of desired thicknesses using atomic layer deposition, followed by a temperature-programmed reduction treatment of the film under H2/N2 atmosphere. This method enables the phase pure synthesis of all three Fe-Pt alloy phases, namely Fe3Pt, FePt, and FePt3, as revealed by in situ x-ray diffraction and x-ray fluorescence measurements. It is also demonstrated that by changing the total thickness of the bilayers while keeping the Pt/(Pt + Fe) atomic ratio constant, the size of the resulting bimetallic nanoparticles can be tuned, as confirmed by scanning electron microscopic measurements.