Modern microbialites in Argentina’s Puna (Central Andes) are considered a reliable tool for understanding the evolution of early life on our planet and developing strategies for detecting life on Mars. The morphological, structural and geochemical variations in these deposits, together with their distribution and architecture, are some of the most important parameters for understanding and characterising them. However, the lack of appropriate cartography and/or the high price to access it, added to the complex geological and geomorphological context in this region, complicate a traditional mapping on a good scale of detail. This paper presents a GIS-based methodology for a detailed mapping and architectural modeling of Las Quínoas microbialitic deposit (Holocene). To meet this objective, the geoprocessing of the information obtained from drone surveys, fieldwork and laboratory work, is carried out using ArcGIS software. The result is a high-resolution reconstruction of the deposit architecture, together with several thematic maps that represent the variation of the morphological, structural and geochemical characteristics of the oncoids (microbialites) with respect to depth and their position in the water body. From an integral point of view, this work provides a new methodological approach for microbialites mapping and improves the survey strategies in Central Andes.