Abstract The impact of extensive changes in land use and climate on species has led to an increasing focus on large-scale conservation planning. However, these plans are often static conservation prescriptions set against a backdrop of rapidly changing environments, which suggests that large-scale information on threats can improve the functionality of planning efforts. Jaguars (Panthera onca) are the focus of a range-wide conservation strategy extending from Mexico to Argentina that consists of jaguar conservation units (JCUs) and modeled corridors. Recent deforestation is a major threat to jaguar populations, but forest loss has not been systematically assessed across the entire jaguar network. In this study, we quantified the amount and rate of deforestation in JCUs and corridors between 2000 and 2012. JCUs lost 37,780 km2 forest (0.93%) at an increasing rate of 149.2 km2 yr−2, corridors lost 45,979 km2 (4.43%) at a decreasing rate of 40.1 km2 yr−2, and levels of forest fragmentation increased in corridors. Protected sections of JCUs and corridors lost less forest than unprotected sections, suggesting efforts to increase protected status of jaguar conservation areas are warranted. Higher deforestation in corridors indicates difficulties in maintaining connectivity of jaguar populations, and suggests the need for increased engagement with communities within corridor landscapes. Assessment of spatial variability of anthropogenic threats within the jaguar network may improve jaguar conservation by informing network prioritization and function.