Studies using ecological niche models highlight the vulnerability of forest species to climate change. This work aimed to analyze the distribution of timber species Aspidosperma desmanthum, Cariniana micranta, Clarisia racemosa, Couratari oblongifolia, and Vouchysia guianensis, which are targets of deforestation, to predict the impacts of climate change and identify areas for their conservation in the Amazon. For this purpose, 37 environmental variables were used, including climatic and edaphic factors. The models were fitted using five algorithms, and their performance was evaluated by the metrics Area Under the Curve (AUC), True Skill Statistic, and Sorensen Index. The deforestation analysis was conducted using data accumulated over a period of 14 years. The study indicated that under the most pessimistic predictions, considering continued high emissions of greenhouse gases (GHGs) from the use of fossil fuels, SSP5–8.5, potential habitat loss for the studied species was more significant. Analyses of the species show that the Western Amazon has a greater climatic suitability area for the conservation of its genetic resources. Further study of the accumulated deforestation over 14 years showed a reduction in area for all species. Therefore, in situ conservation policies and deforestation reduction are recommended for the perpetuation of the analyzed forest species.