This study presents a comprehensive investigation of the unroofed cave above the active Škocjanske Jame water cave and explains the intricate processes that characterize the karst landscape. Despite extensive knowledge of the karst morphology, the precise development stages and timing of formation remained ambiguous. Through detailed multi-proxy sedimentary analyses, we unveil the sedimentary features documenting relict speleogenetic processes and provide insights into regional tectonic events and climatic changes. The cave was filled with two types of sediments: the upper speleothem section and the lower allogenic clastic section. Based on paleomagnetic characteristic and U/Th data, the fill of the unroofed cave is estimated to be between approximately 5 Ma (probably 5.2 to 4.9 Ma) and >773 ka old. Our results reveal a complex interplay of allogenic and autogenic sediments, suggesting a stable catchment over several million years. The dating results indicate deposition in phreatic regime since at least 5 Ma, with the river flowing through the cave until about 2.6 Ma. Our study emphasizes the importance of tectonically-driven uplift phases in cave speleogenesis rather than the importance of Quaternary climate changes. Furthermore, we define the initial stages of the development of the Škocjanske Jame karst system and estimate the time span of the evolution of solution and collapse dolines. This research underscores the importance of integrating geological, hydrological, and chronological approaches to unravel the history of karst landscapes and their implications for understanding dynamic karst processes. The temporal and spatial reconstruction of the development of the unroofed caves provides an insight into the first stages of the present karst system influenced by the sinking river.