Alteration of conventional carbonate stable isotopes (δ18O, δ13C) in cave walls has been shown to be a useful tool to identify cave formation driven by deep-seated processes, i.e., hypogene karstification. If combined with a prior information on the paleowater stable isotope composition, further insights can be obtained on the temperature and the source of the paleowater. Clumped isotope composition (Δ47) of carbonates is an independent measurement of temperature, and if combined with the conventional stable isotopes, can provide information on the paleowater stable isotope composition. On the example of Provalata Cave (N. Macedonia), we apply for the first time, both conventional and clumped stable isotope analysis, and identify two different isotope alteration trends, reflecting two distinct hydrothermal events: an older, hotter one, where isotope alteration was likely related to isotope diffusion, lowering the δ18O values of the carbonate; and a younger one, related to the cave formation by low-temperature CO2-rich thermal waters, with dissolution-reprecipitation as the alteration mechanism, causing decrease in δ18O values, and unexpected increase in δ13C values. The findings are further corroborated by additional insight from optical petrography and cathodoluminescence microscopy, as well as fluid inclusion analysis of secondary calcite crystals related to the cave forming phase.