Previous modeling studies with atmospheric general circulation models and basic land surface schemes to balance energy and water budgets have shown that by removing the natural vegetation over the Amazon, the region's climate becomes warmer and drier. In this study we use a fully coupled Earth system model and replace tropical forests by a distribution of six common tropical crops with variable planting dates, physiological parameters and irrigation. There is still general agreement with previous studies as areal averages show a warmer (+1.4 K) and drier (−0.35 mm day⁻¹) climate. Using an interactive crop model with a realistic crop distribution shows that regions of vegetation change experience different responses dependent upon the initial tree coverage and whether the replacement vegetation is irrigated, with seasonal changes synchronized to the cropping season. Areas with initial tree coverage greater than 80 % show an increase in coupling with the atmosphere after deforestation, suggesting land use change could heighten sensitivity to climate anomalies, while irrigation acts to dampen coupling with the atmosphere.