Understanding how the composition of organic coatings influences their ability to resist surface damage during use remains a challenge. A relevant potential influence is that of cross-linking density. This parameter is frequently used for tailoring the mechanical properties of organic coatings and it manifests itself in terms of scratch resistance. However, the mechanisms that influence scratch resistance are not fully understood. From a thermodynamic perspective, wear of coatings is related to their ability to dissipate friction energy. Hence, it would be reasonable to assume that cross-linking influences the scratch resistance of coatings by influencing their viscoelasticity, as this is one of the parameters that define energy dissipation during shear. This hypothesis was investigated by studying two similar waterborne polyurethane coatings that have different cross-linking properties. The multiple abilities of Atomic Force Microscopy (AFM) were used to characterize the coatings’ scratch resistance, frictional properties, stiffness, adhesiveness and viscoelasticity. Significantly, it was found that monitoring the thermal noise of AFM cantilevers in contact with the coatings was sensitive enough to quantify the effects of cross-linking on their viscoelasticity. Based on this work, cross-linking is proposed to enhance scratch resistance by elastically storing, and eventually releasing, part of the mechanical energy that was transferred to the coatings during shear.