• Salt weathering of tuff was investigated in underground cultural heritage. • Efflorescences and crusts are made of mixed sulfates, mostly hydrated, in part rare. • Salt source and variation are related to lithological variability and stone decay. • Salt occurrence and seasonality depend on microclimate changes in time and space. Salt weathering is one of the most damaging processes affecting stone conservation and represents an extensively debated topic in heritage science. The main subject of previous research is the built heritage, whereas other types of assets are often neglected, such as underground cultural heritage. This paper introduces an investigation of stone decay in the subterranean environment focused on salt weathering, its patterns, compositional features, and variability in time and space, aiming at finding its driving forces in the rock properties and environmental setting. Field explorations and the mineralogical analysis of salt efflorescences and crusts were integrated by the petrographic, geochemical, and petrophysical characterization of the rock substrates, a microclimate monitoring, and the chemical analysis of groundwater and rainwater. The subject of study is the underground archaeological-historical site of Yoshimi Hyaku Ana in Japan, a complex of Kofun tombs of the 6th–7th century and galleries of the WWII era. The site is affected by intense salt weathering, involving efflorescences and crusts composed of mixed soluble sulfates, mostly hydrated: gypsum, alunogen, alum-(Na), halotrichite, epsomite, polyhalite, tamarugite, thenardite, and mirabilite. They derive principally from the dissolution of rock-forming minerals and components (pyrite, glass, feldspars, etc.) from the Miocene volcanic tuffs into which the site is excavated. The tuffs show a certain lithological diversity (e.g., glass amount and chemico-mineralogical composition) that controls the space variability of salt composition. Another major influencing factor is the underground microclimate, which also affects the time variability and seasonality of salt weathering. The innermost underground areas have an extremely high relative humidity (~100%) and are essentially salt-free, whereas, nearby the site entrances, the wider fluctuations of air temperature and humidity create conditions for salt crystallization in the dry winter season and deliquescence in summer. Depending on the solubility of each salt phase, cycles of crystallization/dissolution and hydration/dehydration can occur both seasonally and in the short-term, causing severe stresses to the stone and damage.