It is unquestionable that Colombian armed conflicts have had adverse impacts on the natural environment in the country. Current transitional justice mechanisms offer an opportunity to recognize harm and responsibility, establish restorative sanctions and reparations and adopt public policies for the recovery of ecosystems and prevention of further damage. This article focuses on how transitional justice mechanisms, especially the Special Jurisdiction for Peace, have addressed the effects of armed conflicts on the natural environment. Specifically, it analyzes the criminal characterization of environmental degradation, the question of whether amnesties and pardons could be granted for such conducts, precautionary measures and the implementation of restorative sanctions related to the environment. It presents some challenges regarding the preservation of the natural environment due to the persistence of armed conflicts after the 2016 Peace Accord between the government and the FARC-EP guerrillas, and the sustainability of reparations for victims and prevention of further damage. It also sustains that the developments of current transitional justice mechanisms may have significant influence on ongoing and future peace negotiations with other armed groups and the processes for establishing responsibility for environmental damages.