Acid rain is one of the major contributors to the loss of tropical forest. Although the effects of acid rain in leaf anatomy have been widely studied, its impact on specialized secretory structures remains unknown. The aim of this study was to investigate the morphoanatomical changes in the extrafloral nectaries of Cedrela fissilis in response to simulated acid rain. Each seedling was sprayed with 50 ml of an acidic solution daily for 19 consecutive days. Anatomical and micromorphological changes in the nectaries were described. The treated plants exhibited plasmolysis and disruption of epidermal cells, cell collapse, hypertrophy, plasmolysis, phenolic and starch accumulation in the nectar-secreting cells, and the formation of a wound healing tissue. The results indicate that the nectaries of C. fissilis undergo alterations when exposed to acid rain, which may compromise the functioning of the entire structure and potentially impact plant-insect ecological interactions.