Self-etching primers (SEP), used for adhesion of resin restorations, contain an acidic monomer that is not rinsed off after application; therefore, residual acid could further demineralize dentin, jeopardizing adhesion. This study evaluated whether dentin demineralization continues after a 20-s application of a SEP and also after polymerization of the adhesive. Surface recession was measured, using atomic force microscopy (AFM), between the masked surface and dentin etched with SEP (Clearfil SE Bond) or phosphoric acid (pH 1.94) immediately, 5 min, 2 h or 12 h after application. AFM-based nanoindentations were performed to determine mechanical property profiles across resin-bonded interfaces of two sequence groups: SG 1, where the adhesive was applied and polymerized immediately after application of the primer and specimens were immersed in Hank's solution after 5 min, 2 h and 12 h; or SG 2, where specimens were placed in an incubator before the application of the adhesive, for the same time periods. Significant surface recession occurred over time for all groups, except for SEP before desiccation. Nanoindentations yielded decreased hardness and elastic modulus below the hybrid layer after application of the initial primer, even after polymerization of the adhesive. The results reveal a demineralized dentin zone below the hybrid layer formed by the SEP, not fully protected by the adhesive, which could jeopardize bond strength.