Particulate matter concentrations (PM10, PM2.5, PM1) and microclimatic parameters (air temperature, CO2) were monitored in the Škocjan Caves (Slovenia). The effects of tourist visits on the PM concentrations and the cave’s microclimate are immediate and direct, but these values normalise relatively quickly. The results showed seasonal, diurnal, and spatial differences in all parameters studied. Due to the higher number of visitors, their influence on the cave’s microclimate and PM10 and PM2.5 concentrations is greater in summer than in winter. The measured PM1 levels depend on the ventilation in the cave, as air transport plays an important role in their introduction into the cave. PM consists of minerals of natural origin resulting from the re-suspension of cave sediments due to strong air currents generated by the opening of the doors to tourists and their walks. The second most common influence is the anthropogenic phases originating from maintenance work in the cave, electronic devices, cave lighting and emissions from outside the cave (aerosols from the polluted Reka River, industry, traffic, gypsum waste disposal). In order to upgrade the sustainable use of the UNESCO-listed Škocjan Caves for tourism, we propose regular monitoring of PM and a detailed characterization of individual PMs and their sources, in addition to monitoring of the cave’s microclimate and biology.