Coffee producers in Mesoamerica are already facing some of the expected challenges arising from pressures derived by climate change, principally lowered water supply. Some farmers have implemented strategies of adaptation based on crop diversification, being the introduction of cocoa one of the main alternatives. The focus of this research is to analyse coffee producers’ perceptions on changing from coffee to cocoa as an adaptation strategy. This research tries to find the factors that smallholders take into account when facing the decision of introducing cocoa. Here we simulate the farmers’ response to climate factors and water needs, also considering its relationship with humankind, specially through variables related to economic and social development. Farmers’ perceptions were extracted via a specifically designed questionnaire applied to 219 small coffee producers in the departments of Esteli and Jinotega in Nicaragua. A Multivariate probit econometric model was estimated to analyse diversification through three simultaneous equations—for climatic, economic and social development drivers.  Marginal effects of these drivers were calculated and used to simulate farmers’ response to global change scenarios. Regional distribution of crop diversification probability was mapped considering different global change scenarios. The importance of climatic factors over the decision process is, as data shows, higher than social and economic issues. The environmental implications of this change, such as deforestation, have also been discussed.