Water-borne coatings often contain nanofillers to enhance their mechanical or optical properties. The aggregation of these fillers may, however, lead to undesired effects such as brittle and opaque coatings, reducing their performance and lifetime. By controlling the distribution and structural arrangement of the nanofillers in the coatings and inserting reversible chemical bonds, both the elasticity and strength of the coatings may be effectively improved, while healing properties, via the reversible chemistry, extend the coating’s lifetime. Aqueous dispersions of polymer-core/silica-corona supracolloidal particles were used to prepare water-borne coatings. Polymer and silica nanoparticles were prefunctionalized with thiol/disulfide groups during the supracolloid assembly. Disulfide bridges were further established between a cross-linker and the supracolloids during drying and coating formation. The supracolloidal nanocomposite coatings were submitted to intentional (physical) damages, i.e., blunt and sharp surface scratches or cut through into two pieces, and subsequently UV irradiated to induce the recovery of the damage(s). The viscoelasticity and healing properties of the coatings were examined by dynamic, static, and surface mechanical analyses. The nanocomposite coatings showed a great extent of interfacial restoration of cut damage and surface scratches. The healing properties are strongly related to the coating’s viscoelasticity and interfacial (re)activation of the disulfide bridges. Nanocomposite coatings with silica concentrations below their critical volume fraction show higher in situ healing efficiency, as compared to coatings with higher silica concentration. This work provides insights into the control of nanofillers distribution in water-borne coatings and strategies to increase the coating lifetime via mechanical damage recovery.