Significance Unquantified intermediate-scale heterogeneity in VOC emissions over Amazonia may be a key contributor to the observed discrepancy between measured and modeled VOC concentrations, but in situ measurements for investigating the possibility have been lacking. The measurements presented herein quantify horizontal VOC concentration gradients over different forest subtypes at intermediate scales of several hundred meters. The results suggest that there are biases in both top-down estimates based on satellite or aircraft measurements and bottom-up approaches based on leaf or tower measurements. The results demonstrate how observations collected by UAV-enabled technologies fill a missing niche among leaf-level, tower, aircraft, and satellite scales. Information at this previously unavailable scale is needed for accurate understanding and predictions related to changing forests under climate stress.