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OBJECTIVES This study investigated the ability of modified phosphoric acids containing chlorhexidine (CHX) or grape seed extract (GSE) for promoting simultaneous biomodification during acid etching on bonding properties in caries-affected dentin (CAD). MATERIALS AND METHODS Thirty-two human molars (8 with sound dentin [SD] and 24 naturally CAD) were selected for the study. The SD and CAD were initially exposed, then randomized and etched according to the following groups: (1) SD (SD-CT) and CAD (CAD-CT) both with 37% phosphoric acid, (2) CAD with 2% CHX containing 37% phosphoric acid (CAD-CHX), and (3) CAD with 2% GSE containing 10% phosphoric acid (CAD-GSE). The bonding procedure and composite build-ups were performed after acid etching. Subsequently, they were sectioned in resin-dentin specimens. The specimens were submitted for chemical profiling by micro-Raman, microtensile bond strength (μTBS), failure mode with chemical characterization by FEG/SEM-EDX, and in situ zymography by CLSM. The data from μTBS and CLSM were statistically analyzed (1-way ANOVA and Tukey's test; α = 0.05). RESULTS The highest μTBS results were shown for SD-CT in comparison with all CAD groups (p < 0.001), and the lowest for CAD-CT and CAD-CHX (p < 0.001). The etching with CHX did not increase the μTBS for CAD when compared with CT (p = 0.52). However, the etching with GSE improved significantly the μTBS for CAD when compared with CT and CHX (p < 0.001). The chemical profile detected chemical and structural changes in collagen peaks for CAD-CT, which were not detected when the CAD was etched by modified acids. Also, the poorest hybridization ability was detected in CAD for CT, which was significantly improved with modified acids, especially the GSE, as evaluated by chemical profile and failure mode. A significant reduction of MMP activity on CAD was promoted by modified acids in comparison with CT (both p < 0.001). CONCLUSIONS The GSE-containing acid was able to promote biomodification during the acid etching, increasing the bonding properties and reducing the activity of the MMPs within the hybrid layer. CLINICAL RELEVANCE The use of GSE-containing phosphoric acid can be a promising alternative to improve the bonding performance on caries-affected dentin, since it is capable of biomodifying the dentin during the acid etching, without adding any extra step in bonding procedures.