In most developing countries, there has been a long-standing conflict of interest between using land for agriculture and the conservation of biodiversity. This paper reports on a study of factors influencing farmers’ decisions to integrate trees into their agricultural practice. We also discuss the possibility of protecting and managing planted and naturally regenerating trees on farmland in order to restore degraded land and improve biodiversity. Data were collected from interviews with farmers in the Center-West region of Burkina Faso and analyzed using Principal Component Analysis, multiple linear regression and binary logistic regression. The results show that farmers’ decisions to incorporate trees into their farmland were mainly influenced by silvicultural knowledge and skills, participation in farmers’ groups or other social organizations with an interest in tree conservation, the social value of biodiversity in the rural landscape, and the perceived economic benefits of trees on farmland. The most important factors associated with variation in levels of motivation to conserve trees on farms included household wealth, gender, age, education level, marital status, residence status, farmland size, household size and technical support. We conclude that an agroforestry project will be more successful if the local biophysical conditions and diversity of smallholder socio-economic characteristics and their perceptions, needs and preferences are considered in its design. There is also an immediate need for coordinated development of information and training to raise local community awareness of the potential of agroforestry as well as to disseminate information about adding value to tree products in order to encourage farmers to protect on-farm trees.