Abstract This study explores the role of vegetation biophysical processes (VBPs) in the structure and evolution of the South American monsoon system (SAMS) with an emphasis on the precipitation field. The approach is based on comparing ensemble simulations by the National Centers for Environmental Prediction general circulation model (GCM) in which the land surface parameterization in one ensemble includes an explicit representation of vegetation processes in the calculation of surface fluxes while the other does not [GCM/Simplified Simple Biosphere Model (SSiB) and GCM/Soil, respectively], but with similar monthly mean surface albedo and initial soil moisture. The ensembles consist of five pairs of 1-yr integrations differing in the initial conditions for the atmosphere. The results show that, during the austral summer, consideration of explicit vegetation processes does not alter the monthly mean precipitation at the planetary scale. However, at continental scales, GCM/SSiB produces a more successful simulation of SAMS than GCM/Soil. The improvement is particularly clear in reference to the seasonal southward displacement of precipitation during the onset of the SAMS and its northward merging with the intertropical convergence zone during the monsoon mature stage, as well as better monthly mean austral summer precipitation over the South American continent. The changes in surface water and energy balances and circulation in October (monsoon onset) and December (the start of the monsoon mature stage) were analyzed for a better understanding of the results and mechanisms involved. It was found that the major difference between the simulations is in the partitioning of latent heat and sensible heat fluxes (i.e., different Bowen ratio), which produced different latitudinal and longitudinal thermal gradients at the surface. A stronger sensible heat flux gradient between continent and ocean in the GCM/SSiB simulation helped generate an enhanced ventilation effect, which lowered moist static energy (MSE) over the northeast coast of South America leading to stronger counterclockwise turning of the low-level wind from the Atlantic Ocean toward the continent during the premonsoon and early monsoon stages, modifying moisture flux convergence (MFC). It was further identified that the seasonality of savanna and shrublands to the south and east of the Amazon rain forest contributed to the variability of heating gradients and influenced the SAMS onset and its northward merge with the ITCZ at the early monsoon mature stage. The comparison of the differences between precipitation, evaporation, advection of MSE, and MFC based on simulations using two different land parameterizations suggested that the VBP modulated the surface water budget, but its impact on precipitation was determined by the changes in circulation via changes in heat gradient and MSE.