Shallow clouds are prone to appear over deforested surfaces whereas deep clouds, much less frequent than shallow clouds, favor forested surfaces. Simultaneous atmospheric soundings at forest and pasture sites during the Rondonian Boundary Layer Experiment (RBLE-3) elucidate the physical mechanisms responsible for the observed correlation between clouds and land cover. We demonstrate that the atmospheric boundary layer over the forested areas is more unstable and characterized by larger values of the convective available potential energy (CAPE) due to greater humidity than that which is found over the deforested area. The shallow convection over the deforested areas is relatively more active than the deep convection over the forested areas. This greater activity results from a stronger lifting mechanism caused by mesoscale circulations driven by deforestation-induced heterogeneities in land cover.