Porous stone materials can be affected by lithobiontic communities’ colonization responsible for physical-chemical processes that lead to their biodeterioration. In urban areas with high levels of atmospheric pollution, in the aesthetical decay of facades due to soiling by particulate matter deposition, the development of biological films must be considered. The biodeterioration processes affecting the joint mortar used on the limestone facades of the Formerly Workers Hospital of Maudes (Madrid, Spain) and its contribution to facades soiling are studied. Lichen thalli are directly involved in the material disruption and foster significantly the degree of darkening. While limestone darkening is very heterogeneous and mainly responds to its interaction with air pollutants, for the joint mortar it is much more homogeneous and, in areas of higher humidity and with no direct pollution exposure, is due to a biofilm development. In all other areas where joint mortar shows darkening, this is mainly because of its interaction with air pollutants.