Marine conservation strategies often allocate considerable resources towards the establishment and management of Marine Protected Areas (MPAs) with the expectation they will both provide sustainable fisheries that support community livelihoods and well being (including food security), as well as biodiversity benefits for coral reef ecosystems. This rigourous, interdisciplinary study tests the common rhetoric that increases in ecosystem benefits lead to increases in social benefits. We investigate both the ecological and social impacts of MPAs, and examine short-term synergies and tradeoffs that have occurred among objectives. We applied a quasi-experimental design to control for observable bias in MPA placement and outcomes to disentangle MPA impacts from broader social-ecological trends in human well-being and coral reef conditions in Eastern Indonesia. Baseline and repeat data was collected at six MPAs at over 150 coral reef monitoring sites, and 112 settlements within and outside of MPAs. Ecological and social MPA impacts vary across indicators and in both magnitude and direction of impact. We apply a decision-theoretic framework to examine the synergies and tradeoffs among and between the ecological and social MPA impacts, finding evidence for trade-offs and synergies between MPA social and ecological objectives, which vary at different spatial scales. These insights will inform ongoing adaptive management and marine spatial planning and policy, as well as advance our understanding of the dynamics of complex social ecological systems.