This report details the use of the CFT at the smallholder level in Kenya on 25 coffee farms. Since the coffee is produced in agroforestry systems, the results show the added benefit of having shade trees present in the system. In addition to the on-farm emissions, processing emissions from the cooperative are also presented. This paper also highlights some of the unique challenges of collecting/analyzing data at the smallholder scale, as well as data related to tree systems in general.