Substitutional doping of transition metal dichalcogenides (TMDs) may provide routes to achieving tunable p-n junctions, bandgaps, chemical sensitivity, and magnetism in these materials. In this study, we demonstrate in-situ doping of monolayer molybdenum disulfide (MoS2) with manganese (Mn) via vapor phase deposition techniques. Successful incorporation of Mn in MoS2 leads to modifications of the band structure as evidenced by photoluminescence and x-ray photoelectron spectroscopy, but this is heavily dependent on the choice of substrate. We show that inert substrates (i.e. graphene) permit the incorporation of several percent Mn in MoS2, while substrates with reactive surface terminations (i.e. SiO2 and sapphire) preclude Mn incorporation and merely lead to defective MoS2. The results presented here demonstrate that tailoring the substrate surface could be the most significant factor in substitutional doping of TMDs with non-TMD elements.