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Studying land use change in protected areas (PAs) located in tropical forests is a major conservation priority due to high conservation value (e.g., species richness and carbon storage) here, coupled with generally high deforestation rates. Land use change researchers use a variety of land cover products to track deforestation trends, including maps they produce themselves and readily available products, such as the Global Forest Change (GFC) dataset. However, all land cover maps should be critically assessed for limitations and biases to accurately communicate and interpret results. In this study, we assess deforestation in PA complexes located in agricultural frontiers in the Amazon Basin. We studied three specific sites: Amboró and Carrasco National Parks in Bolivia, Jamanxim National Forest in Brazil, and Tambopata National Reserve and Bahuaja-Sonene National Park in Peru. Within and in 20km buffer areas around each complex, we generated land cover maps using composites of Landsat imagery and supervised classification, and compared deforestation trends to data from the GFC dataset. We then performed a dissimilarity analysis to explore the discrepancies between the two remote sensing products. Both the GFC and our supervised classification showed that deforestation rates were higher in the 20km buffer than inside the PAs and that Jamanxim National Forest had the highest deforestation rate of the PAs we studied. However, GFC maps showed consistently higher rates of deforestation than our maps. Through a dissimilarity analysis, we found that many of the inconsistencies between these datasets arise from different treatment of mixed pixels or different parameters in map creation (for example, GFC does not detect reforestation after 2012). We found that our maps underestimated deforestation while GFC overestimated deforestation, and that true deforestation rates likely fall between our two estimates. We encourage users to consider limitations and biases when using or interpreting our maps, which we make publicly available, and GFC's maps.