Colombia is recognized as a megadiverse country. According to the National Evaluation of Biodiversity and Ecosystem Services (ES) of Colombia 2021, Colombia encompasses 50% of the world's moorlands, 18% of the territory contains Andean forests, 7% dry forests and 39% are tropical forests located in the Amazon and Pacific regions. Also, aquifers and wetlands cover more than 26% of the territory, making Colombia exceptionally rich in water resources. However, many of these essential ecosystems are being affected by anthropogenic interventions and actions derived from different activities. Here, we summarize the main socio-environmental conflicts in Colombia, derived from mining activities, hydrocarbons, land use changes and water resource management, to propose a conceptual methodological route for the prevention and resolution of conflicts. The first stage is the evaluation of the environmental impacts; here the main aspects for the approval and execution of an activity or project in the territory are explained. The second stage, communication with local communities, explains the process for implementing the prior consultation, which seeks community participation in decision about their territory is guaranteed. In the third stage, the participation mechanisms during the project development are explained. Finally, the fourth stage, includes the process for monitoring the project by the environmental authority. The implementation of this route seeks to help strengthen the compliance of the mechanisms established in the national regulations when addressing a socio-environmental conflict that results from a particular project or human activity. In addition, recommendations and alternatives for decision-making in the implementation of projects in Colombia are presented.