Understanding how to improve decision makers’ use of scientific information across their different scales of management is a core challenge for narrowing the gap between science and conservation practice. Here, we present a study conducted in collaboration with decision makers that aims to explore the functionality of the mechanisms for scientific input within the institutional setting of the National Protected Area Network of Peru. First, we analyzed institutional mechanisms to assess the scientific information recorded by decision makers. Second, we developed two workshops involving scientists, decision makers and social actors to identify barriers to evidence-based conservation practice. Third, we administered 482 questionnaires to stakeholders to explore social perceptions of the role of science and the willingness to collaborate in the governance of protected areas. The results revealed that (1) the institutional mechanisms did not effectively promote the compilation and application of scientific knowledge for conservation practice; (2) six important barriers hindered scientific input in management decisions; and (3) stakeholders showed positive perceptions about the involvement of scientists in protected areas and expressed their willingness to collaborate in conservation practice. This collaborative research helped to (1) identify gaps and opportunities that should be addressed for increasing the effectiveness of the institutional mechanisms and (2) support institutional changes integrating science-based strategies for strengthening scientific input in decision-making. These insights provide a useful contextual orientation for scholars and decision makers interested in conducting empirical research to connect scientific inputs with operational aspects of the management cycle in other institutional settings around the world.