The Bastion of San Pedro is part of the defensive infrastructure projected by Spanish colonizers in San Francisco de Campeche City, in order to protect the city and their inhabitants from pirates who ravaged the region during the XVIth and XIXth centuries. The bastion is a masonry structure built by using calcareous materials according the Spanish procedures from the edge. Since its construction, it has been under the synergetic interaction of natural and anthropogenic factors that promote degradation. In this study optical microscopy (MO) and scanning electron microscopy coupled to a dispersive analysis system (SEM/EDS) were used in order to analyze the stratigraphic profile of mortar weathered samples collected from walls of the Bastion of San Pedro. According the results, the samples were formed by three substrata: an upper external layer in contact with the environment (100 to 300 µm), the other one is an inner layer with thickness around 100 to 400 µm. The last substrate was formed by the mortar matrix composed by elements such as C, O, Ca, Si and Al, that indicate their mineral origin. By the other hand, it is important to note that the upper layer contained higher proportion of C respect to the other layers. It is probably major consequence of biomass encrustation rather that atmospheric pollution according to the particular environmental conditions surrounding the building.