The explicit coupling at meter and second scales of vegetation's responses to the atmospheric‐boundary layer dynamics drives a dynamic heterogeneity that influences canopy‐top fluxes and cloud formation. Focusing on a representative day during the Amazonian dry season, we investigate the diurnal cycle of energy, moisture and carbon dioxide at the canopy top, and the transition from clear to cloudy conditions. To this end, we compare results from a large‐eddy simulation technique, a high‐resolution global weather model, and a complete observational data set collected during the GoAmazon14/15 campaign. The overall model‐observation comparisons of radiation and canopy‐top fluxes, turbulence, and cloud dynamics are very satisfactory, with all the modeled variables lying within the standard deviation of the monthly aggregated observations. Our analysis indicates that the timing of the change in the daylight carbon exchange, from a sink to a source, remains uncertain and is probably related to the stomata closure caused by the increase in vapor pressure deficit during the afternoon. We demonstrate quantitatively that heat and moisture transport from the subcloud layer into the cloud layer are misrepresented by the global model, yielding low values of specific humidity and thermal instability above the cloud base. Finally, the numerical simulations and observational data are adequate settings for benchmarking more comprehensive studies of plant responses, microphysics, and radiation.