This paper builds on critiques that call for a more nuanced and contextualised understanding of conditions that affect HIV prevention by looking at West Papuan women's experiences of prevention of mother-to-child transmission services. Drawing on qualitative, ethnographic research with indigenous women and health workers, the paper demonstrates that women experience poor-quality HIV education and counselling, and that indigenous practices and concerns are largely not addressed by HIV services. We attribute this to a combination of national anti-indigenous and anti-separatist political concerns with donor-led interventions that result in limited localisation and reduced effectiveness of HIV prevention measures. In West Papua, services are needed that enhance cooperation and shared commitment, and that acknowledge and work to overcome existing inequalities, ethnic tensions and discrimination in the health system. Beyond Indonesia, donor-led HIV programmes and interventions need to balance avoidance of politically sensitive issues with complicity in perpetuating health inequalities. Translating global health interventions and donor priorities into locally compelling HIV prevention activities involves more than navigating local cultural and religious beliefs. Programme development and implementation strategies that entail confronting structural questions as well as social hierarchies, cleavages and silences are needed to render more effective services; strategies that are inherently political.