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Illegal logging is a major driver of tropical deforestation, accounting for the majority of timber harvested in many tropical countries and degrading many protected areas, due to both weak law enforcement capacity and corruption. Commercial logging is illegal in Peru’s Allpahuayo-Mishana National Reserve, a state protected area, but clandestine logging operations persist and affect its biodiversity, including the endemic bird species associated with its rare Amazonian white-sand forests. We examined the effects of illegal logging operations on white-sand forest understory bird communities as sentinels of biodiversity. We sampled birds with mist nets at 12 study sites in unlogged forest and forest regenerating between 1 and 10 years after timber harvest, capturing and releasing 348 birds representing 54 species in 16 families. Forest structure differed significantly between forest treatments, with canopy cover in logged forest significantly lower than in unlogged forest. All avian foraging guilds tested (including ant followers, other insectivores, frugivores, granivores, and nectarivores) responded significantly to changes in one or more forest structure characteristics we measured. The abundance of ant followers and other insectivores was positively correlated with canopy cover, while granivore abundance was positively correlated with subcanopy cover, and both frugivore and nectarivore abundance was negatively correlated with the numbers of trees in white-forest stands. We also took a rare opportunity to compare avian foraging guilds and relative abundance using capture data collected at the same white-sand forest sites in both 2005 and 2023. Over this 18-year period, the total number of understory birds and ant followers in particular declined, whereas other insectivores increased with time since logging. Our results demonstrate that logging has significant influences on white-sand forest habitat structure and bird community dynamics for decades after logging events. Illegal logging threatens forests and wildlife in many tropical protected areas, and we recommend their managers prioritize both preventing illegal logging and mitigating its negative effects to effectively conserve biodiversity.