A systematic attempt has been made to correlate the thermal and rheological behavior of thermosetting powder coating systems with their surface structure build-up. Epoxy-based and polyurethane-based powder coating systems, which displayed surface matting and surface wrinkling, were examined. Firstly, the evolution of the complex viscosity was correlated with the degree of conversion. Secondly, the structure build-up on the surface of the coatings was investigated with a confocal laser scanning microscope at different temperatures, and was shown to be closely related to the degree of conversion and to the evolution of the complex viscosity. The surface structure is built up just before gelation point and continues to evolve after gelation. Differences were observed in the surface structure build-up between the two systems during curing but the surface structure was not changed during the cooling process. These experimental results lead to a better understanding of the development of surface topography and morphology and provide valuable information for the development of new powder coating systems.