Understanding the electron transport through transition-metal dichalcogenide (TMDC)-based semiconductor/metal junctions is vital for the realization of future TMDC-based (opto-)electronic devices. Despite the bonding in TMDCs being largely constrained within the layers, strong Fermi-level pinning (FLP) was observed in TMDC-based devices, reducing the tunability of the Schottky barrier height. We present evidence that metal-induced gap states (MIGS) are the origin for the large FLP similar to conventional semiconductors. A variety of TMDCs (MoSe2, WSe2, WS2, and MoTe2) were investigated using high-spatial-resolution surface characterization techniques, permitting us to distinguish between defected and pristine regions. The Schottky barrier heights on the pristine regions can be explained by MIGS, inducing partial FLP. The FLP strength is further enhanced by disorder-induced gap states induced by transition-metal vacancies or substitutionals at the defected regions. Our findings emphasize the importance of defects on the electron transport properties in TMDC-based devices and confirm the origin of FLP in TMDC-based metal/semiconductor junctions.