His research is related to the study of impacts of land use/cover change (LUCC) on biodiversity loss and habitat fragmentation in tropical dry forest environments.
Sánchez-Azofeifa uses advanced technology, including remote sensing and phenology towers, to evaluate land use and cover change in Mesoamerica.
His research focuses on the efficacy of creating protected areas (National Parks and Biological Reserves) and use of Environmental Services payment methods to control tropical deforestation.
In addition, his research examines remote sensing (multispectral and hyperspectral) in connection with Primary Productivity (PP), Leaf Area Index (LAI), Photosynthetic Active Radiation (PAR) and biodiversity, particularly in tropical secondary dry forests.
Sánchez-Azofeifa's most cited paper is his 2006 Nature article, "Widespread amphibian extinctions from epidemic disease driven by global warming.