We evaluate the Community Atmosphere Model Version 5 (CAM5) with a higher-order turbulence closure scheme, named Cloud Layers Unified By Binomials (CLUBB), and a Multiscale Modeling Framework, referred as the “super-parameterization” (SP) with two different microphysics configurations to investigate their influences on rainfall simulations over Southern Amazonia. The two different microphysics configurations in SP are the one-moment cloud microphysics without aerosol treatment (SP1) and two-moment cloud microphysics coupled with aerosol treatment (SP2).