Recent research on two-dimensional (2D) transition metal dichalcogenides (TMDCs) has led to remarkable discoveries of fundamental phenomena and to device applications with technological potential. Large-scale TMDCs grown by chemical vapor deposition (CVD) are now available at continuously improving quality, but native defects and natural degradation in these materials still present significant challenges. Spectral hysteresis in gate-biased photoluminescence (PL) measurements of WSe₂ further revealed long-term trapping issues of charge carriers in intrinsic defect states. To address these issues, we apply here a two-step treatment with organic molecules, demonstrating the “healing” of native defects in CVD-grown WSe₂ and WS₂ by substituting atomic sulfur into chalcogen vacancies. We uncover that the adsorption of thiols provides only partial defect passivation, even for high adsorption quality, and that thiol adsorption is fundamentally limited in eliminating charge traps. However, as soon as the molecular backbone is trimmed and atomic sulfur is released to the crystal, both bonds of the sulfur are recruited to passivate the divalent defect and the semiconductor quality improves drastically. Time-dependent X-ray photoelectron spectroscopy (XPS) is applied here together with other methods for the characterization of defects, their healing, leading energies and occupation. First-principles calculations support a unified picture of the electronic passivation of sulfur-healed WSe₂ and WS₂. This work provides a simple and efficient method for improving the quality of 2D semiconductors and has the potential to impact device performance even after natural degradation.