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Tuning the Fermi level (EF) in two-dimensional transition metal dichalcogenide (TMDC) semiconductors is crucial for optimizing their application in (opto-)electronic devices. Doping by molecular electron acceptors and donors has been suggested as a promising method to achieve EF-adjustment. Here, we demonstrate that the charge transfer (CT) mechanism between TMDC and molecular dopant depends critically on the electrical nature of the substrate as well as its electronic coupling with the TMDC. Using angle-resolved ultraviolet and X-ray photoelectron spectroscopy, we reveal three fundamentally different, substrate-dependent CT mechanisms between the molecular electron acceptor 1,3,4,5,7,8-hexafluoro-tetracyano-naphthoquinodimethane (F6TCNNQ) and a MoS2 monolayer. Our results demonstrate that any substrate that acts as charge reservoir for dopant molecules can prohibit factual doping of a TMDC monolayer. On the other hand, the three different CT mechanisms can be exploited for the design of advanced heterostructures, exhibiting tailored electronic properties in (opto-)electronic devices based on two-dimensional semiconductors. Doping of 2D semiconductors by electron acceptor or donor molecules has been suggested as a method to optimize their properties for electronic devices. Here, the authors identify three distinct charge transfer mechanisms that depend on the substrate and yield different doping efficiencies. [ABSTRACT FROM AUTHOR]