Frequently, the management of natural areas and the aspirations of the indigenous communities linked to these areas are in conflict. A recurrent theme is that the conservation objectives of natural areas are not always compatible with the expectations of the communities. In this article, three cases are analyzed in Chile: (1) the Aymarás communities associated with Lauca National Park, (2) the Atacameños communities linked to The Flamencos National Reserve, and (3) the Mapuches-Huilliches communities, adjacent to Chiloé National Park. The general objective is to compare the conflicts, perceptions, and expectations of the indigenous communities associated with these natural areas. The study used an exploratory and qualitative design, utilizing key informants and representatives of the communities. The conclusions obtained for the three groups are relatively similar. All the communities demand ancestral rights of land ownership and a stronger role in decision making regarding land use. Nevertheless, they have an increasingly positive perception of the institution that administers the natural areas (The Chilean Forest Service-CONAF); the reasons for this perception include the recent indigenous participation approach used in the planning and management of the natural areas and the technical assistance received from the institution. However, resentment persists in the communities regarding the lack of participation in the original decision to establish the natural areas. Thus, the challenge to strengthen the trust with the communities in achieving mutual goals acquires special importance.