Abstract Background Plague remains a public health problem in specific areas located in Bolivia, Brazil, Ecuador and Peru. Its prevention and control encompasses adequate clinical management and timely laboratory diagnosis. However, understanding communities’ interaction with its surrounding ecosystem as well as the differences between community members and institutional stakeholders regarding the root causes of plague might contribute to understand its endemicity. We aim at bridging the traditionally separate biological and social sciences by elucidating communities’ risk perception and identifying knowledge gaps between communities and stakeholders. This approach has been used in other areas but never in understanding plague endemicity, nor applied in the Latin American plague context. The objectives were to identify (i) plague risk perception at community level, (ii) perceived social and environmental determinants of plague endemicity, and (iii) institutions that need to be involved and actions needed to be taken as proposed by stakeholders and community members. The study was performed in 2015 and took place in Ascope rural province, La Libertad Region, in Peru, where the study areas are surrounded by intensive private sugarcane production. Methods We propose using a multi-level discourse analysis. Community households were randomly selected (n = 68). Structured and semi-structured questionnaires were applied. A stakeholder analysis was used to identify policy makers (n = 34). In-depth interviews were performed, recorded and transcribed. Descriptive variables were analyzed with SPSS®. Answers were coded following variables adapted from the Commission on Social Determinants of Health and analyzed with the assistance of ATLAS.ti®. Results Results showed that risk perception was low within the community. Policy-makers identified agriculture and sugarcane production as the root cause while community answers ranked the hygiene situation as the main cause. Stakeholders first ranked governmental sectors (education, housing, agriculture and transport) and the community prioritized the health sector. Social surveillance and improving prevention and control were first cited by policy-makers and community members, respectively. Conclusions The determinants of plague endemicity identified by the two groups differed. Similarly, actions and sectors needed to be involved in solving the problem varied. The gaps in understanding plague root causes between these two groups might hinder the efficiency of current plague prevention and control strategies.