The perceptions and values that local communities have towards protected areas are of great value for the improvement of these territories’ management. Such perceptions and values are often absent in the conservation planning process, particularly in those privately protected areas that are established in areas where the land tenure system is based not only on ownership but also on customary uses. Drawing on qualitative and quantitative data obtained through semi-structured interviews with key stakeholders and members of communities surrounding a privately protected area in southern Ecuador, we identify that the level of collaboration with the managers, the distance to the protected area, the percentage of untitled land, and the dependence on the resources (customary uses) are among the variables affecting these perceptions and values. Positive perceptions towards protected areas and naturalistic values are developed among those who collaborate with the protected area managers, whereas negative perceptions, and a mix of naturalistic and biospheric values are developed among those who have a sense of a lack of attention to social needs although supporting nature conservation at the same time. The evidence presented shows the importance of matching local peoples’ expectations with conservation goals during the establishment of a protected area.