Understanding the electronic contact between molybdenum disulfide (MoS2) and metal electrodes is vital for the realization of future MoS2-based electronic devices. Natural MoS2 has the drawback of a high density of both metal and sulfur defects and impurities. We present evidence that subsurface metal-like defects with a density of ∼1011 cm–2 induce negative ionization of the outermost S atom complex. We investigate with high-spatial-resolution surface characterization techniques the effect of these defects on the local conductance of MoS2. Using metal nanocontacts (contact area < 6 nm2), we find that subsurface metal-like defects (and not S-vacancies) drastically decrease the metal/MoS2 Schottky barrier height as compared to that in the pristine regions. The magnitude of this decrease depends on the contact metal. The decrease of the Schottky barrier height is attributed to strong Fermi level pinning at the defects. Indeed, this is demonstrated in the measured pinning factor, which is equal to ∼0.1 at defect locations and ∼0.3 at pristine regions. Our findings are in good agreement with the theoretically predicted values. These defects provide low-resistance conduction paths in MoS2-based nanodevices and will play a prominent role as the device junction contact area decreases in size.