Preventive conservation requires monitoring and control of the parameters involved in the deterioration process, mainly temperature and relative humidity. It is important to characterise an archaeological site prior to carrying out comparative studies in the future for preventive conservation, either by regular studies to verify whether the conditions are constant, or occasional ones when the boundary conditions are altered. There are numerous covered archaeological sites, but few preventive conservation works that give special attention to the type of cover installed. In particular, there is no background of microclimatic studies in sites that are in the ground and, as in the Plaza de l'Almoina (Valencia, Spain), are buried and partially covered by a transparent roof. A large effect of the transparent cover was found by the sensors located below this area, with substantial increases in temperature and a decrease in the relative humidity during the day. Surrounding zones also have values above the recommended temperature values. On the other hand, the influence of a buried water drainage line near the site is notable, causing an increase in relative humidity levels in the surrounding areas. Multivariate statistical analyses enabled us to characterise the microclimate of the archaeological site, allowing future testing to determine whether the conservation conditions have been altered.