Flavan‐3‐ol monomers are the building blocks of proanthocyanidins (PACs), natural compounds from plants shown to mediate specific biologic activities on dentin. While the stereochemistry of the terminal flavan‐3‐ols, catechin (C) versus epicatechin (EC), impacts the biomechanical properties of the dentin matrix treated with oligomeric PACs, structure–activity relationships driving this bioactivity remain elusive. To gain insights into the modulatory role of the terminal monomers, two highly congruent trimeric PACs from Pinus massoniana only differing in the stereochemistry of the terminal unit (Trimer‐C vs. Trimer‐EC) were prepared to evaluate their chemical characteristics as well as their effects on the viscoelasticity and biostability of biomodified dentin matrices via infrared spectroscopy and multi‐scale dynamic mechanical analyses. The subtle alteration of C versus EC as terminal monomers lead to distinct immediate PAC‐trimer biomodulation of the dentin matrix. Nano‐ and micro‐dynamic mechanical analyses revealed that Trimer‐EC increased the complex moduli (0.51 GPa) of dentin matrix more strongly than Trimer‐C (0.26 GPa) at the nanoscale length (p < 0.001), whereas the reverse was found at the microscale length (p < .001). The damping capacity (tan δ) of dentin matrix decreased by 70% after PAC treatment at the nano‐length scale, while increased values were found at the micro‐length scale (~0.24) compared to the control (0.18 ; p < .001). An increase in amide band intensities and a decrease of complex moduli was observed after storage in simulated body fluid for both Trimer‐C and Trimer‐EC modified dentin. The stereochemical configuration of the terminal monomeric units, C and EC, did not impact the chemo‐mechanical stability of dentin matrix.