How do the relationships between the concept of being indigenous and the processes of ethnoeducation manifest in southwestern Colombia? This ethnographic study explores the complexities of constructing ethnic identity among the indigenous peoples of Nariño, focusing on the implementation of educational programs driven by a population perspective. By questioning the foundations of ethnoeducation from the late 20th century to the early 21st century, we establish a dialogue among various institutional agents within the broader framework of ethnic-based social organization. We also examine the historical relationships, institutional archaisms, and contemporary challenges faced by ethnic educational processes in Nariño. We conclude with insights into the construction of ethnic identity and its implications for the social order governing the interactions between community members and government representatives. We conceptualize the relationship between the State, school, and ethnic identity as a fundamental part of Colombia’s modern project, which has been in development since the republican era. The institutional framework has fluctuated between protectionist, paternalistic, and cultural assimilation policies. However, the current threats to the physical and cultural survival of ancestral peoples must be addressed through the State’s institutional mechanisms and governance technologies. These mechanisms are designed to tackle the challenges of interculturality within a complex and often contradictory framework of relationships.