Agroecological markets are determinants for the success of agroecology because the transition from agroecological production is not enough to make agri-food systems sustainable. The present research was carried out between 2015 and 2016, where a group of indicators were designed to manage the sustainability of the Red de Mercados Agroecológicos de Bogotá Región (RMABR; Spanish for the Agroecological Market Network of the Bogotá Region). The MESMIS (Spanish for Framework for the Evaluation of natural resource Management Systems incorporating Sustainability Indicators) methodology was applied due to its wide use in agroecosystem sustainability assessments. This resulted in the development of twelve indicators classified into four sustainability attribute groups. Each indicator was evaluated on a three-degree scale: target situation or goal, acceptable, and unacceptable. The four markets evaluated evince varied levels of sustainability, with greater socio-economic indicator challenges, such as the number of consumers linked and the income–cost relation of the markets. The results provided a methodology that can be easily employed, and thus guarantee effective use in the management of agroecological markets sustainability.