This study uses aircraft observations over the Republic of Benin from the African Monsoon Multidisciplinary Analyses (AMMA) campaign to investigate the impact of vegetation heterogeneities on the dynamics within the planetary boundary layer, such as convection, transport, and mixing. Isoprene, a biogenic volatile organic compound emitted primarily by woody vegetation, was used as a tracer for transport to link the land surface to the boundary layer properties. Associated to planetary boundary layer (PBL) temperature gradients at vegetation boundaries, a persistent mesoscale organization of the winds which controlled patterns in the formation of cumulus congestus clouds was observed. A strong relationship among PBL temperatures, meridional wind velocity, isoprene concentrations, and fraction of forest or shrub cover was found, corroborating the land surface forcing of the observed dynamics. The observations show that the convergence zones tended to occur on the southern edge of warm surface and atmospheric anomalies. The northerly synoptic wind appears to have increased the coherency of the southerly part of the mesoscale flow and displaced the convergence zones southward. The relationships between the PBL potential temperatures and the meridional wind and isoprene concentrations were spatially coherent down to wavelengths of 10 and 8 km, respectively. A seasonal climatology of visible satellite data shows enhanced cloud cover in the afternoon over cropland, suggesting that the results presented are not limited to this case study but are of climatological significance in the region.