Environmental impact assessment systems are preventive management instruments whose main objective is to include environmental considerations in the processes and activities accompanying economic growth in a nation. The influence of these systems in the conservation of biodiversity is fundamental, since within the evaluation process, they enable identifying and evaluating potential environmental impacts, as well as defining reparations, compensations, or mitigations. Halting the loss of biodiversity caused by human activities and climate change is a global objective. Chile is also facing this challenge, considering its status of Biodiversity Hotspot, projections associated with climate change, and the outstanding issues that the Environmental Impact Assessment System (SEIA) shows regarding biodiversity conservation. The latest, based on the lack of strategic view when considering issues such as the territorial scope of the environmental impacts generated by the projects, under a systemic and transversal approach. This research analyses the main changes experienced since the creation of SEIA, and compares this system with other evaluation systems used in Latin America. National statistics on investment projects potentially affecting the conservation of biodiversity are given. Two issues are addressed to guide discussion of the operational changes that should be encouraged by the Chilean government, namely: 1) internalising the importance of protecting biodiversity beyond current regulations, and; 2) introducing improvements in environmental legislation that could indirectly lead to improvements in SEIA. The research concludes on the importance of strengthening the Strategic Environmental Assessment (SEA) and its integration with the SEIA, in order to encourage better project designs by including sustainability from the beginning.