Abstract Coherent structures, such as updrafts, downdrafts/shells, and environmental subsidence in the boundary and cloud layers of shallow convection, are investigated using a new classification method. Using large-eddy simulation data, the new method first filters out background turbulence and small-scale gravity waves from the coherent part of the flow, composed of turbulent coherent structures and large-scale transporting gravity waves. Then the algorithm divides this coherent flow into “updrafts,” “downdrafts/shells,” “subsidence,” “ascendance,” and four other flow structures using an octant analysis. The novel method can systematically track structures from the cloud-free boundary layer to the cloud layer, thus allowing systematic analysis of the fate of updrafts and downdrafts. The frequency and contribution of the coherent structures to the vertical mass flux and transport of heat and moisture can then be investigated for the first time. Updrafts, subsidence, and downdrafts/subsiding shells—to a lesser extent—are shown to be the most frequent and dominant contributors to the vertical transport of heat and moisture in the boundary layer. Contrary to previous perspective, environmental subsidence transport is shown to be weak in the cloud layer. Instead, downdrafts/shells are the main downward transport contributors, especially in the trade inversion layer. The newly developed method in this study can be used to better evaluate the entrainment and detrainment of individual—or an ensemble of—coherent structures from the unsaturated boundary layer to the cloud layer.