The impact of climate change in intermediate cities is a topic of growing interest on Latin America. This study analyzed the influence of climate in the city of Pasto, Colombia. Based on several land use planning methodologies, we defined the main urban elements that affect the city’s territorial dynamics. Subsequently, we employed a structural analysis to identify the main relationships among the urban elements. Using direct and indirect classification based on the method of cross-impact matrices applied multiplication for a classification (MICMAC) and the Delphi method, we determined the dependencies and influences of the urban elements integrated in a systemic model of 12 positive and 8 negative loops that relate climate, energy, and culture as power elements over the city’s economy, health, education, environment, functionality, demography, and security, all of which are articulated by governance as the key element, with results applicable to other cities in the region.