The organization of cave invertebrate communities reflects the combined effects of spatial separation among caves, internal habitat heterogeneity, and key environmental features such as shelter availability and trophic resource diversity. Although these factors are recognized as drivers of subterranean biodiversity, their relative influence remains poorly understood in semiarid cave systems, largely due to the scarcity of studies explicitly testing these mechanisms under strong climatic constraints. In this study, we propose that the structure of cave invertebrate assemblages is shaped by both surface-derived (epigean) and subterranean (hypogean) environmental drivers, and that the relative importance of these factors varies across spatial scales in limestone outcrops underlying Caatinga vegetation. To test this hypothesis we surveyed 18 caves distributed across 14 limestone outcrops, sampling two spatial scales that included 26 cave sectors (30 m2 each) and 78 quadrats (1 m2 each). In total, 1228 individuals representing 127 species, including eight troglobitic morphotypes, were recorded. Community composition differed significantly among caves, indicating marked spatial structuring. Variation in assemblage composition was significantly influenced by geographic distance between caves, the presence of guano deposits, and shelter availability within cave interiors. At the mesoscale, species richness exhibited a negative relationship with relative humidity, whereas no environmental variables significantly influenced richness at the microscale. Collectively, these results highlight the importance of spatial scale and fine-scale environmental heterogeneity in structuring subterranean communities, reinforcing patterns documented in cave ecosystems. This study provides new insights into how ecological mechanisms operate under climatically restrictive conditions, with implications for the conservation of karst landscapes.