To evaluate the biomodification ability of lignin used as pre-treatment in human dentin before the application of an etch-and-rinse adhesive. Experimental hydroethanolic solutions with different cross-linking agents were used: 6.5% proanthocyanidins (PAC, from grape-seed extract); 2% cardanol (CARD, from cashew-nut shell liquid); lignin (LIG, from eucalyptus) at 1, 2 or 4% concentrations. The negative control (NC) was ethanol 50 v%. Extracted molars were prepared, and dentin microtensile bond strength (μTBS) was evaluated after 24 h water storage or 10,000 thermocycling aging. Further specimens were processed for SEM nanoleakage, micropermeability confocal microscopy evaluation and in situ degree of conversion (DC) through micro-Raman spectroscopy. Demineralized dentin sticks were submitted to a three-point bending test to evaluate the elastic modulus (E) before and after 1 min biomodification using the tested solutions. Moreover, it was also evaluated the mass changes and hydroxyproline (HYP) release after 4-weeks of water storage. Vibrational collagen crosslinking identification was evaluated through micro-Raman spectroscopy. The results were analyzed by analysis of variance (ANOVA) and Tukey’s test (α = 0.05). A significant reduction in μTBS was observed in groups NC (p < 0.001) and CARD (p = 0.026). LIG-4% showed no significant reduction in μTBS after aging (p = 0.022). Nanoleakage micrographs showed hybrid layer protection with all agents, but reduced micropermeability was attained only with lignin. Polymerization was negatively affected in the presence of all tested cross-linking agents, except LIG-1%. Lignin and cardanol increased the dentin E values, but only lignin reduced the mass loss in dentin specimens. Effective collagen crosslinking (1117 cm⁻¹ and 1235 cm⁻¹) was detected for all agents. HYP release was significantly lower with LIG-1% than NC (p < 0.001). Lignin was able to perform collagen cross-linking and prevent the degradation of unprotected dentin collagen, thereby improving the bonding performance of the composite restorations performed in this study.