Understanding growth, grain boundaries (GBs), and defects of emerging two-dimensional (2D) materials is key to enabling their future applications. For quick, nondestructive metrology, many studies rely on confocal Raman spectroscopy, the spatial resolution of which is constrained by the diffraction limit (∼0.5 μm). Here we use tip-enhanced Raman spectroscopy (TERS) for the first time on synthetic MoSe2 monolayers, combining it with other scanning probe microscopy (SPM) techniques, all with sub-20 nm spatial resolution. We uncover strong nanoscale heterogeneities in the Raman spectra of MoSe2 transferred to gold substrates [one near 240 cm–1 (A1′), and others near 287 cm–1 (E′), 340 cm–1, and 995 cm–1], which are not observable with common confocal techniques and appear to imply the presence of nanoscale domains of MoO3. We also observe strong tip-enhanced photoluminescence (TEPL), with a signal nearly an order of magnitude greater than the far-field PL. Combining TERS with other SPM techniques, we find that GBs can cut into larger domains of MoSe2, and that carrier densities are higher at GBs than away from them.