Governments in developing counties often promote intercropping (crops intercropped with fruit trees on cultivated land) schemes in order to improve smallholders’ income. However, the implementation of such schemes is often hindered by inappropriate institutional environments and inefficient project management. It is important to assess the impacts of such intercropping programs, especially since such a cultivation strategy can often align closely with smallholders’ livelihood strategies, particularly in poor and remote rural regions. This paper attempts to assess the impact of an intercropping program on participants’ incomes in rural Xinjiang (China), and to explore the possible shortcomings in the program’s design and implementation. We apply a propensity score matching method, based on a survey dataset of 352 households, supplemented with descriptive analysis based on our anecdotal field observations. The findings demonstrate that the intercropping program had negative effects on the incomes that participants derived from farming, their off-farm income and their gross income. Overall, participants experienced significant losses of income. Anecdotal observations show that land tenure insecurity played a crucial role in negating the anticipated income improvement effect of this program. Farmer’s perceptions that they have limited security of tenure made them reluctant to invest the necessary time and resources to make the new cropping systems a success, while the available subsidies only partially covered the costs involved. In addition, the program led to a significant drop in yields of field crops as the trees were competing for a limiting and fixed supply of irrigation water.