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Contact engineering on monolayer layer (ML) semiconducting transition metal dichalcogenides (TMDs) is considered the most challenging problem towards using these materials as a transistor channel in future advanced technology nodes. The typically observed strong Femi level pinning induced in part by the reaction of the source/drain contact metal and the ML TMD frequently results in a large Schottky barrier height, which limits the electrical performance of ML TMD field-effect transistors (FETs). However, at a microscopic level, little is known about how interface defects or reaction sites impact the electrical performance of ML TMD FETs. In this work, we have performed statistically meaningful electrical measurements on at least 120 FETs combined with careful surface analysis to unveil contact resistance dependencies on the interface chemistry. In particular, we achieved a low contact resistance for ML MoS2 FETs with ultra-high vacuum (UHV, 3×10-11 mbar) deposited Ni contacts, ~500 ohm·μm, which is 5 times lower than the contact resistance achieved when deposited at high vacuum (HV, 3×10-6 mbar) conditions. These electrical results strongly correlate with our surface analysis observations. X-ray photoelectron spectroscopy (XPS) revealed significant bonding species between Ni and MoS2 under UHV conditions compared to HV. We also studied the Bi/MoS2 interface under UHV and HV deposition conditions. Different from the case of Ni, we do not observe a difference in contact resistance or interface chemistry between contacts deposited under UHV and HV. Finally, this article also explores the thermal stability and reliability of the two contact metals employed here.