Background: Currently, most of the world’s population lives in cities, and the rapid urbanization of the population is driving increases in the demand for products, goods and services. To effectively design policies for urban sustainability, it is important to understand the trends of flows in energy and materials as they enter and leave a city. This knowledge is essential for determining the key elements characterizing future urban growth and addressing future supply challenges. Methods: This paper presents an analysis of the energy and material flows in the city of Bogotá over the time span from 2001 to 2017. Urban flows are also characterized in terms of their temporal evolution with respect to population growth to compare and identify the changes in the main input flows, wealth production, emissions and waste in the city. Results: The results of the analysis are then compared with those for other selected large urban agglomerations in Latin America and worldwide to highlight similarities and make inferences. The results show that in Bogotá, there was a decrease in some of the material flows, such as the consumption of water and the generation of discharge, in recent years, while there was an increase in the consumption of energy and cement and in the production of CO2 emissions and construction materials. Solid waste production remained relatively stable. With respect to the other large cities considered, we observe that the 10-year growth rates of the flows with respect to population growth are lower in Bogotá, particularly when compared with the other urban agglomerations in Latin America. Conclusions: The findings of this study are important for advancing characterizations of the trends of material and energy flows in cities, and they contribute to the establishment of a benchmark that allows for the definition and evaluation of the different impacts of public policy while promoting the sustainability of Bogotá in the coming decades.