The unique characteristics of graphene have generated much excitement due to its utility across a variety of applications. One of the principal issues inhibiting the development of graphene technologies pertains to difficulties in engineering high-quality metal contacts on graphene. In this regard, the thermal transport at the metal/graphene interface plays a significant role in the overall performance of devices. Here, we demonstrate the use of electron beam produced plasmas to chemically modify graphene and how these modifications can be used to tune the thermal transport s across metal-graphene interfaces. We show that the operating conditions of the plasma can be adjusted to control the character and quantity of chemical moieties at the interface. Typically, when changes in the surface chemistry favor an increase in adhesion between the graphene and metal, the thermal boundary conductance can be notably improved. Interestingly, the conventional approach of adding a titanium "wetting layer" to improve metal adhesion did not improve the thermal boundary conductance at gold contacts.