This study investigates the institutional transformations within Indonesia’s research ecosystem, focusing on the impacts of the National Research and Innovation Agency (BRIN) establishment and the subsequent Work From Office (WFO) policy on the Association of Indonesian Researchers (PPI). The research aims to evaluate these impacts and propose an adaptive institutional revitalization model. Employing a mixed-methods approach, a total of 150 online questionnaires were distributed across 21 regional branches of PPI between February and March 2025. Of these, 87 were completed and valid for analysis, representing a 58% response rate. Findings reveal that the WFO policy has led to a significant decline in member participation, coordination difficulties across regions, and weakened collaboration with local partners such as regional governments and universities. A SWOT analysis of three revitalization options—full agglomeration, bounded agglomeration, and non-BRIN integration—identified a hybrid model as the most adaptive and widely supported alternative (41.5%). This hybrid model combines selective structural efficiency with inclusive membership expansion, aiming to preserve regional identity, enhance collaboration, and strengthen organizational legitimacy. The study offers key insights for developing adaptive governance frameworks rooted in epistemic justice, digital accountability, and cross-sectoral collaboration, applicable to professional organizations navigating decentralization and institutional disruption. The proposed hybrid model serves as a strategic reference for achieving organizational resilience and fostering a more inclusive national innovation ecosystem.