A light-accessed scanning tunneling microscope (STM) is a powerful spectroscopic tool that enables chemical analysis at the single molecular level, but it requires highly precise optical alignments to pinpoint the nano-scale tunneling gap, leaving experimental challenges. Here we present straightforward procedures to align the optical setup for STM-luminescence and STM-based tip-enhanced Raman spectroscopy (TERS) performed with a reflection geometry in an ultrahigh vacuum chamber. Observing real-space images of the metal tip apex through a spectrograph set to the zeroth-order diffraction enables “in situ” optimization of the detection path and introduction of the excitation light of TERS to the nanogap. The best spatial overlap with the nanogap can be achieved by monitoring plasmon-enhanced, low-frequency inelastic scattering of the metal. This protocol allows us to overcome such difficulties in STM-based spectroscopy and facilitates physicochemical study of single adsorbates on nontransparent substrates.