Despite many available models at different reactor length scales, no models exist for designing homogeneous–heterogeneous reactors from first principles by linking molecular with macroscopic scales. Hybrid algorithms, based on a domain decomposition method, are proposed to couple a continuum fluid-phase transport/reaction model with a new efficient, real-time surface Monte Carlo model suitable for stiff problems. These algorithms properly treat surface heterogeneities and morphology and provide the exact boundary condition to the continuum fluid-phase model. In this way, molecular-scale information is integrated into a macroscopic chemical system. The methods are applied at atmospheric pressure to a stagnant boundary layer near a catalytic surface where heterogeneities are caused by adsorbate–adsorbate interactions. Both steady-state and transient simulations are performed. Such numerical methods have the potential for microscopic control of chemical processes through macroscopic control of experimental parameters. Applications to homogeneous–heterogeneous processes such as catalytic reactors, control of morphology of solid materials with atomic resolution, and corrosion processes are also discussed.