Evidences of microbial colonizations were observed in Altamira Cave, Spain. These consisted of distinct small coloured colonies, both on walls and ceiling, mainly located in the area near the cave entrance, which progressed until reaching the Polychromes Hall. The colonizations were characterized by a high morphological and microstructural variability and related to biomineralization processes. Two main types of CaCO3 deposits were related to the colonies: rosette- or nest-like aggregates of rhombohedral calcite crystals, and spheroid to hemispheroid CaCO3 elements. Colonies distribution seems to be controlled by microenvironmental conditions inside the cavity. The areas of the cave showing higher temperature, relative humidity, and CO2 concentration fluctuations presented a minor biomineralization capability.