Improving the longevity of composite restorations has proven to be difficult when they are bonded to dentin. Dentin demineralization leaves collagen fibrils susceptible to enzymatic digestion, which causes breakdown of the resin-dentin interface. Therefore, measures for counteracting the enzymatic environment by enhancing dentin collagen's resistance to degradation have the potential to improve the durability of dental composite restorations. This study aimed to evaluate the effects of polyphenol-rich extracts and a chemical cross-linker on the cross-linking interaction, resistance to digestion, and endogenous matrix metalloproteinase (MMP) activities of dentin collagen under clinically relevant conditions. Ten-microm-thick films were cut from dentin slabs of non-carious extracted human third molars. Following demineralization, polyphenol-rich extracts-including grape seed (GSE), green tea (GTE), and cranberry juice (CJE)-or chemical cross-linker carbodiimide with n-hydroxysuccinimide (EDC/NHS) were applied to the demineralized dentin surfaces for 30 s. The collagen cross-linking, bio-stabilization, and gelatinolytic activities of MMPs 2 and 9 were studied by using Fourier-transform infrared spectroscopy, weight loss, hydroxyproline release, scanning/transmission electron microscopy, and in situ zymography. All treatments significantly increased resistance to collagenase degradation and reduced the gelatinolytic MMP activity of dentin collagen compared to the untreated control. The CJE- and GSE-treated groups were more resistant to digestion than the GTE- or EDC/NHS-treated ones (p < 0.05), which was consistent with the cross-linking interaction found with FTIR and the in situ performance on the acid-etched dentin surface found with SEM/TEM. The collagen films treated with CJE showed the lowest MMP activity, followed by GSE, GTE, and, finally, EDC/NHS. The CJE-treated dentin collagen rapidly increased its resistance to digestion and MMP inhibition. An application of CJE as short as 30 s may be a clinically feasible approach to improving the longevity of dentin bonding in composite restorations.