Semiconducting transition metal dichalcogenides (TMDs) are promising materials for future electronic and optoelectronic applications. However, their electronic properties are strongly affected by peculiar nanoscale defects/inhomogeneities (point or complex defects, thickness fluctuations, grain boundaries, etc.), which are intrinsic of these materials or introduced during device fabrication processes. This paper reviews recent applications of conductive atomic force microscopy (C-AFM) to the investigation of nanoscale transport properties in TMDs, discussing the implications of the local phenomena in the overall behavior of TMD-based devices. Nanoscale resolution current spectroscopy and mapping by C-AFM provided information on the Schottky barrier uniformity and shed light on the mechanisms responsible for the Fermi level pinning commonly observed at metal/TMD interfaces. Methods for nanoscale tailoring of the Schottky barrier in MoS2 for the realization of ambipolar transistors are also illustrated. Experiments on local conductivity mapping in monolayer MoS2 grown by chemical vapor deposition (CVD) on SiO2 substrates are discussed, providing a direct evidence of the resistance associated to the grain boundaries (GBs) between MoS2 domains. Finally, C-AFM provided an insight into the current transport phenomena in TMD-based heterostructures, including lateral heterojunctions observed within MoxW1–xSe2 alloys, and vertical heterostructures made by van der Waals stacking of different TMDs (e.g., MoS2/WSe2) or by CVD growth of TMDs on bulk semiconductors.