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CONDESAN, through the Project "Knowledge generation and capacity building as an adaptation response to environmental changes in the Andes" (CIMA Project), financed by the Swiss Agency for Development and Cooperation (COSUDE), has promoted, together with the Secretaría General de la Comunidad Andina, the generation and management of knowledge on Andean ecosystems in scenarios of environmental change, as well as the articulation of knowledge through the strengthening of thematic research networks. Its main contributions have revolved around the development of methodological protocols for studying Andean ecosystems and rural systems, which have been validated in different environmental and social contexts, the generation of baselines at a number of sites along the Andes, and the promotion of arrangements with various stakeholders to establish comprehensive and sustainable monitoring systems. As part of the knowledge generation component, this document is the first in a series of methodological protocols generated by the CIMA Project as an effort to study and understand the dynamics of Andean ecosystems through the adoption of standards in data collection, processing, and management. Specifically, this protocol deals with how to estimate and monitor carbon contents and flows in high Andean ecosystems in environmental gradients. This protocol is a "living document" and, as such, constitutes a first version that we hope can be used as a mechanism for discussion with the scientific community, the monitoring programs of the Ministries of Environment of the Andean countries and international cooperation, with the aim of collecting suggestions that will allow us to enrich and generate a new version, nourished from the practical experiences of its application in different environmental and social contexts of the Andes.