Collagen is the most important structure of the hybrid layer, and chemical alteration to its structure could be gainful during bonding procedures. Aim: To evaluate the influence of two natural cross-linking agents (pomegranate peel extract [PP], and Apple peel extract [AP]) compared to chlorohexidine 2% [CHX on the shear bond strength (SBS) of sound and demineralized dentin before and after aging. Materials and Methods: 160 sound human premolars were collected and their occlusal surfaces were ground flat to expose dentin. Eighty teeth were submitted to cariogenic challenge by pH cycling to induce demineralized dentin [DD] after those teeth were randomly divided according to the dentin treatment protocol: chlorohexidine 2 % solution (CHX solution, Consepsis, Ultradent USA), pomegranate peel extract 10% solution (PP, Naturalin Bio-Resources Co., Ltd, Lu-Valley Enterprise Square. Changsha, City. Hunan Province. China), apples peel extract 10% solution (AP, Naturalin Bio-Resources Co., Ltd, Lu-Valley Enterprise Square. Changsha, City. Hunan Province. China) and the control group without any treatment. Then each group was further subdivided into two subgroups the first one was evaluated after 24 hours water storage and the second one after six months of water storage. Data were statistically analyzed by repeated measures Analysis of Variance (ANOVA) to study the effect of material, substrate, storage and their interaction on shear bond strength. Bonferroni’s post-hoc test was used for pair-wise comparisons when the ANOVA test is significant. The significance level was set at P ≤ 0.05. The interaction between the tested variables had a statistically significant effect on mean shear bond strength. PP scored the statistically highest mean shear bond strength. There was no statistically significant difference between CHX and AP; both showed lower mean values. While the control showed the lowest. Conclusion: Chemical alteration to the dentin matrix endorsed by PP and AP lead to enhance in the shear bond strength. The application of natural collagen cross-linkers during bonding procedures may be an innovative approach to enhance dentin bond strength properties