This paper describes the extension of arecently developed numerical solver for the Landau-LifshitzNavier-Stokes (LLNS) equations to binary mixtures in threedimensions. The LLNS equations incorporate thermal fluctuations intomacroscopic hydrodynamics by using white-noise fluxes. Thesestochastic PDEs are more complicated in three dimensions due to thetensorial form of the correlations for the stochastic fluxes and inmixtures due to couplings of energy and concentration fluxes (e.g.,Soret effect). We present various numerical tests of systems in andout of equilibrium, including time-dependent systems, anddemonstrate good agreement with theoretical results and molecularsimulation.