In caves, the absence of natural light in deeper regions starkly contrasts with the entrance areas, which still exhibit a light gradient extending into the cave interior. This interplay with the structural gradient of the environment potentially exerts distinct influences on invertebrate communities residing in different cave light zones. To investigate this, we formulated a hypothesis positing that communities within distinct cave light zones respond differently to habitat structure and microclimatic conditions. Our approach involved a spatial multi-scale sampling of invertebrates and the application of statistical analyses to contrast the responses of communities inhabiting photic and aphotic zones. Photic zone richness is influenced by factors such as air moisture, resource availability, root presence, and shelter diversity. In contrast, the richness of communities in aphotic zones is shaped by resource availability, the presence of roots, branches, and distance from the cave entrance. As expected, the richness in the photic zone surpasses that of the deeper regions, highlighting the challenges faced by invertebrates attempting to establish themselves in the aphotic zone. The species composition of faunal communities varied predictably from the entrance to the aphotic zone, and the three most important factors driving this variation were geographic distance, humidity, and distance from the entrance. The composition between these cave zones differs significantly, primarily due to the high number of obligate cave species predominantly inhabiting the aphotic region. Indeed, communities associated with different cave zones exhibit distinct responses to resource, microclimatic, and structural variables.