As marine ecosystems decline globally, scientists recommend increasing the coverage of marine protected areas (MPAs), but many are not effectively managed to deliver benefits. Community integration into MPA decision-making can increase management effectiveness by supporting behaviour change, but this poses implementation challenges. We examine differences in adaptive capacity, community engagement, and perceived MPA benefits using interviews and focal group meetings with two fishing communities from MPAs with different management strategies and geographic settings: a centrally managed MPA in Kenya and a co-managed MPA in Tanzania. We hypothesized that perceptions of MPA benefits and MPA support would be higher among fishers and fish vendors in the more collaboratively designed system in Tanzania, and supported by greater adaptive capacity. Indeed, far fewer Kenyan participants (37%) felt they benefited from the MPA compared to Tanzanian participants (95%). However, agency and trust were largely similar and challenges existed in both systems that reduced collaborative action including low interaction/communication between staff and community, internal leadership challenges, and social conflict. We identified pathways towards improved co-management that transcend systems: institutional prioritization of community integration, investment in community leadership, mapping social networks during MPA establishment, and adequate staffing and operational budgets.