Global assessments demonstrate that as a conservation measure protected areas (PAs) are incomplete, and tend to be poorly documented in the international scientific literature, hindering the assessment of their scientific and policy foundations. The step from mapping priority areas for biodiversity conservation based on scientific information to formulating the practical tools for conserving biological diversity is critical; several key aspects such as legislative frameworks, multi-scale politics and socioeconomic realities must be taken into account. With the planet's human population continuing to grow, this step is all the more crucial, as the designation of PAs is increasingly being forced alongside the development frontier. This paper examines the process of reserve establishment in the case of the Allpahuayo-Mishana National Reserve (AMNR) (Peruvian Amazonia). On the basis of interviews, document analysis and media studies, a series of actions and reactions worked to shape the ultimate categorization and management plan of the AMNR. While scientific knowledge played a central role in the initial selection of the AMNR site, a number of critical aspects such as estimated environmental services, unresolved land entitlements, use values and multi-scale politics needed to be addressed in order to meet the originally set objective of biodiversity conservation. The importance of several biophysical features of the AMNR was initially emphasized as a key argument for conservation, whereas potential benefits of the AMNR (such as environmental services, particularly at the regional scale) proved to be the ultimate driving factor. Between the AMNR's official establishment in 1999 and its approved categorization and management plan in 2004 and 2005, respectively, a substantial shift in argumentation was witnessed. This change was particularly influential in that, contrary to what was initially expected, the livelihood requirements of local communities that were strongly linked to land entitlements and natural resources management came to play an essential role in both the categorization process and in the elaboration of the management plan of the Reserve. The AMNR was only effectively established because of this shift in emphasis.