Subterranean environments, characterized by features such as relative stability, are widely regarded as valuable natural laboratories for studying ecological and evolutionary processes. This stability is often assumed to shape biodiversity dynamics and community structure over time. Accordingly, it is expected that faunal composition, along with the influence of substrate on invertebrate communities, remains consistent. To test this assumption, we applied a standardized methodology to assess potential changes in subterranean communities across seven limestone caves. Two sampling events, conducted five years apart, were used to evaluate whether these communities are influenced by habitat structure and how their responses evolve over time. Our analysis focused on detecting temporal shifts in community dynamics by comparing two constructed models and examining variations in faunal composition. While invertebrate richness remained stable, we observed significant changes in faunal composition, high temporal beta diversity, and distinct community responses to substrate structure. These results suggest that subterranean environments possess ecological carrying capacity, maintaining richness while exhibiting shifts in community composition. Moreover, the cave substrate is continually remodeled, influencing community responses in distinct ways. In conclusion, this study highlights the non-stationary nature of subterranean ecosystems and emphasizes the importance of utilizing multiple biodiversity metrics to enhance scientific understanding and inform effective management strategies. Investigating temporal dynamics is essential for identifying ecological processes and evaluating their impacts on ecosystem functionality.