Vacancies in atomically thin molybdenum disulfide play an essential role in controlling its optical and electronic properties, which are crucial for applications in sensorics, catalysis or electronics. For this reason, defect engineering employing thiol-terminated molecules is used to heal and/or functionalise defective nanosheets. In this work, CVD-grown MoS2 with different defect densities was functionalised with three molecules: 4-aminothiophenol (ATP), biphenyl-4-thiol (BPT) and 4-nitrothiophenol (NTP). The molecules’ efficacy in functionalising MoS2 was probed by X-ray photoelectron, Raman and photoluminescence spectroscopy. The results show that exposing a defective single layer of MoS2 to either ATP, BPT or NTP molecules heals the defects, however the chemical structure of these molecules affects the optical response and only for BPT the photoluminescence intensity increases.