The ecological footprint of cities is the largest on the planet. Consequently, understanding the scope and limitations of recent methodologies that promote urban environmental sustainability has become increasingly relevant. This article analyzes the implementation process of two methodologies, the ICP (Prosperous City Index) of UN-Habitat and the PCES (Emerging and Sustainable Cities Program) of the Inter-American Development Bank (IDB) in intermediate cities of the Global South. The text begins by reviewing the major trends that have characterized the urban environmental agenda over the last decades as well as the evolution of the term environmental sustainability. Secondly, it presents the research methodology, based on the participation of the authors in the application of the ICP and the PCES in 6 intermediate cities of Mexico and on a comparative analysis of the scope and results obtained in the different stages of these methodologies. In the development section, three categories to group the successes and areas of opportunity of the ICP and the PCES, are defined: integrated and interrelated diagnoses between various urban dimensions and measurements; comparability between cities and monitoring over time that allow the elaboration of actions/policies at the regional or national levels; and a multi-stakeholder and strategic approach that encourages greater interaction between social, public, and private actors that impact on urban territories. It is concluded that these methodologies will continue to have a limited impact as long as they do not promote both, profound changes towards a plural and inclusive form of governance that reduces power asymmetries as well as paradigm shifts on the interdependent relationships between humans and nature.