This paper attempts to examine the role of agroforestry in improving crop yield of small-scale agriculture in the region of Volcanic Highlands of Rwanda. We conducted a survey to a random sample of 401 crop growers, including 305 agroforestry adopters and 95 non-adopters, selected from the study area. An econometric model that lowers the heterogeneity between the treatment and the control groups was specified and estimated. Results revealed a considerable difference in farm yields between agroforestry practitioners and non-practitioners. The adoption of agroforestry appears to have a good impact on small-scale agricultural yield, even though this effect is not statistically significant. Results also show that factors including farm investment cost, market accessibility, cooperative membership and return of plan leftovers to the soil have a significantly substantial effect on farm productivity. On the other hand, farm experience and cultivated land area have a detrimental but considerable impact on farm productivity. Based on the research findings, governmental institutions and development associates should promote and hasten the adoption of agroforestry structures, start increasing support for agroforestry adoption through proximity to extension services and accessibility of high-quality plant seedlings, support for the sustainability of farm cooperatives along with financial support for enhancing farm investments and guarantee a continuous and increased market access to crop farmers so as to ensure sustainable sources of farm investments.