The peculiar microclimate inside cultural hypogeal sites needs to be carefully investigated. This study presents a methodology that aimed at providing a user-friendly assessment of the frequently occurring hazards in such sites. A Risk Index was specifically defined as the percentage of time for which the hygrothermal values lie in ranges that are considered to be hazardous for conservation. An environmental monitoring campaign that was conducted over the past ten years inside the Mithraeum of the Baths of Caracalla (Rome) allowed for us to study the deterioration before and after a maintenance intervention. The general microclimate assessment and the specific conservation risk assessment were both carried out. The former made it possible to investigate the influence of the outdoor weather conditions on the indoor climate and estimate condensation and evaporation responsible for salts crystallisation/dissolution and bio-colonisation. The latter took hygrothermal conditions that were close to wall surfaces to analyse the data distribution on diagrams with critical curves of deliquescence salts, mould germination, and growth. The intervention mitigated the risk of efflorescence thanks to reduced evaporation, while promoting the risk of bioproliferation due to increased condensation. The Risk Index provided a quantitative measure of the individual risks and their synergism towards a more comprehensive understanding of the microclimate-induced risks.