Two-dimensional boron monolayers (i.e., borophene) hold promise for a variety of energy, catalytic, and nanoelectronic device technologies due to the unique nature of boron-boron bonds. To realize its full potential, borophene needs to be seamlessly interfaced with other materials, thus motivating the atomic-scale characterization of borophene-based heterostructures. Here, we report the vertical integration of borophene with tetraphenyldibenzoperiflanthene (DBP) and measure the angstrom-scale interfacial interactions with ultrahigh-vacuum tip-enhanced Raman spectroscopy (UHV-TERS). In addition to identifying the vibrational signatures of adsorbed DBP, TERS reveals subtle ripples and compressive strains of the borophene lattice underneath the molecular layer. The induced interfacial strain is demonstrated to extend in borophene by ∼1 nm beyond the molecular region by virtue of 5 Å chemical spatial resolution. Molecular manipulation experiments prove the molecular origins of interfacial strain in addition to allowing atomic control of local strain with magnitudes as small as ∼0.6%. In addition to being the first realization of an organic/borophene vertical heterostructure, this study demonstrates that UHV-TERS is a powerful analytical tool to spectroscopically investigate buried and highly localized interfacial characteristics at the atomic scale, which can be applied to additional classes of heterostructured materials.