This article examined the unequal political representation of Muslims within the bureaucracy and legislature of Southwest Papua during the Special Autonomy era, despite their comprising a substantial share of the province’s population. Addressing the limited scholarly attention to minority political negotiation within asymmetrical autonomy regimes, this study explored how Muslim political participation extended beyond formal representation through what was conceptualized as compensatory participation—the mobilization of non-electoral channels and social capital to sustain political influence. Employing a qualitative descriptive-exploratory design, data were collected through in-depth interviews, participant observation, and document analysis involving Muslim actors in the bureaucracy, religious organizations, and civil society, and analyzed using the Miles and Huberman interactive model. The findings revealed persistent underrepresentation in the Regional House of Representatives and strategic bureaucratic positions, alongside evidence that Muslim actors built political influence through education, religious organizations such as Muhammadiyah and Nahdlatul Ulama, and interfaith dialogue, despite recurring resistance framed around Islamization narratives. The article argued that inclusive governance in Southwest Papua emerged from the interplay of formal representation, bureaucratic performance, and interfaith social capital, positioning compensatory participation as a key mechanism through which minority groups expanded political influence while maintaining social cohesion.