A growing number of researchers are employing participatory research approaches to address social determinants of health. Despite evidence supporting school-based participatory action research (PAR) approaches as powerful health intervention strategies and recent calls to assess the implementation of PAR processes and outcomes, there is a paucity of research that addresses the meaning of sustainability in participatory health interventions in schools. This case study addresses some of the complexities that emerge when partners with a variety of goals and experiences engage in participatory action research (PAR) within complex institutions. We describe two PAR initiatives within a pragmatic intervention in two middle schools aimed at improving the school environment to promote school engagement and connectedness among adolescents, highlighting perspectives from PAR facilitators and school administrators. Findings underscore complexities of participatory research approaches, including the dynamic and iterative nature of the intervention and limited resources to support collaboration, and stress the role of alignment to existing systems and processes and the need to shift roles and responsibilities in navigating complexities to achieve sustainability. Ultimately, we (re)conceptualize the meaning of sustainability in participatory interventions as a process that is shifting and inseparable from the collaborative, reflective practices characteristic of participatory approaches.