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This study aims to examine the effect of a-tomatine, a new matrix metalloproteinase inhibitor for dentistry, as a surface pretreatment on the bonding strength of different types of dentine via in vitro and in silico methods. The binding efficacy of both a-tomatine and chlorhexidine to MMP-2, 8, and 9 was evaluated through molecular docking and dynamics analyses. For microtensile testing (µTBS), specimens (n = 84) were categorized into two groups based on the type of dentin: sound (SD) and eroded (ED) (n = 42). Each group was further divided into three subgroups according to the utilization of surface pretreatment agents (1.5 µM of tomatine, 2% chlorhexidine (CHX), and the control). Composite buildups were gradually created via a three-step etch-and-rinse technique. The specimens were sectioned into sticks and subsequently subjected to µTBS after aging for either 24 h (n = 7) or 6 months (n = 7). The data were subjected to analysis using two-way ANOVA with a Bonferroni correction post hoc test. The significance level was evaluated at a minimum of p < 0.05. According to molecular docking and dynamic simulation analyses, a-tomatine exhibits a higher affinity for MMP-2, -8, and -9 enzymes compared to chlorhexidine. Lower µTBS values were observed in all ED groups compared to the SD groups. Following 24-h aging, the CHX application in both the SD and ED groups achieved lower µTBS values compared to the control group (p < 0.01 and p > 0.05, respectively). The most favorable results were consistently achieved across all the subgroups subjected to a-tomatine applications (p < 0.05). a-tomatine is a more effective MMP inhibitor than chlorhexidine in terms of preserving bond strength values over time and its capacity to bind to MMP-2,8, and 9 for inhibition.